<link>https://cgm.uni-frankfurt.de/</link></image><item><title>Customizing Hugo</h1> <article> <h1>Customizing Hugo</h1> <p>Mon, 01 Jan 0001 00:00:00 +0000</p> <p>View the full docs at </p> </article> <article> <h1>Project Structure</h1> <p>Mon, 01 Jan 0001 00:00:00 +0000</p> <h2 id="folder-structure">Folder Structure</h2> <p>There are <strong>4 main folders for Hugo-based sites</strong>:</p> <ul> <li><code>content/</code> for your Markdown-formatted content files (homepage, etc.) <ul> <li><code>_index.md</code> the homepage (<strong>Hugo requires that the homepage and archive pages have an underscore prefix</strong>)</li> </ul> </li> <li><code>assets/</code> <ul> <li><code>media/</code> for your media files (images, videos) <ul> <li><code>icons/custom/</code> upload any custom SVG icons you want to use</li> </ul> </li> </ul> </li> <li><code>config/_default/</code> for your site configuration files <ul> <li><code>hugo.yaml</code> to configure Hugo (site title, URL, Hugo options, setup per-folder page features)</li> <li><code>module.yaml</code> to install or uninstall Hugo themes and plugins</li> <li><code>params.yaml</code> to configure Hugo Blox options (SEO, analytics, site features)</li> <li><code>menus.yaml</code> to configure your menu links (if the menu is enabled in <code>params.yaml</code>)</li> <li><code>languages.yaml</code> to configure your site’s language or to set language-specific options in a multilingual site</li> </ul> </li> <li><code>static/uploads/</code> for any files you want visitors to download, such as a PDF</li> <li><code>go.mod</code> sets the version of Hugo themes/plugins which your site uses</li> </ul> <h2 id="hugo-file-naming-convention">Hugo File Naming Convention</h2> <p>Hugo gives us two options to name standard page files: as <code>TITLE/index.md</code> or <code>TITLE.md</code> where <code>TITLE</code> is your page name.</p> <p>The page name should be lowercase and using hyphens (<code>-</code>) instead of spaces.</p> <p>Both approaches result in the same output, so you can choose your preferred approach to naming and organizing files. A benefit to the folder-based approach is that all your page’s files (such as images) are self-contained within the page’s folder, so it’s more portable if you wish to share the original Markdown page with someone.</p> <p>The homepage is a special case as <strong>Hugo requires the homepage and listing pages to be named</strong> <code>_index.md</code>.</p> <h2 id="docs-navigation">Docs Navigation</h2> <p>The docs navigation is automatically generated based on the content in the <code>docs/</code> folder and is sorted alphabetically.</p> <p>The order of pages can be changed by adding the <code>weight</code> parameter in the front matter of your Markdown files.</p> <p>In the example below, the <code>example.md</code> page will appear before the <code>test.md</code> page as it has a lower <code>weight</code>:</p> <p>Page <code>example.md</code>:</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-yaml" data-lang="yaml"><span class="line"><span class="cl"><span class="nn">---</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="nt">title</span><span class="p">:</span><span class="w"> </span><span class="l">My Example</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="nt">weight</span><span class="p">:</span><span class="w"> </span><span class="m">1</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="nn">---</span><span class="w"> </span></span></span></code></pre></div><p>Page <code>test.md</code>:</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-yaml" data-lang="yaml"><span class="line"><span class="cl"><span class="nn">---</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="nt">title</span><span class="p">:</span><span class="w"> </span><span class="l">My Test</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="nt">weight</span><span class="p">:</span><span class="w"> </span><span class="m">2</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="nn">---</span><span class="w"> </span></span></span></code></pre></div> </article> <article> <h1>Configuration</h1> <p>Mon, 01 Jan 0001 00:00:00 +0000</p> <p>The configuration of your site can be found in <code>config/_default/</code>.</p> <h2 id="full-documentation">Full Documentation</h2> <p>See </p> <h2 id="navigation">Navigation</h2> <h3 id="menu">Menu</h3> <p>See </p> <h2 id="left-sidebar">Left Sidebar</h2> <p>Links are automatically generated from the structure of your content directory. Simply add a folder to nest a page.</p> <h3 id="extra-links">Extra Links</h3> <p>Additional links can be added under the <code>sidebar</code> section of your <code>config/_default/menus.yaml</code>:</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-yaml" data-lang="yaml"><span class="line"><span class="cl"><span class="nt">menu</span><span class="p">:</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="w"> </span><span class="nt">sidebar</span><span class="p">:</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="w"> </span>- <span class="nt">name</span><span class="p">:</span><span class="w"> </span><span class="s2">"Need help?"</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="w"> </span><span class="nt">params</span><span class="p">:</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="w"> </span><span class="nt">type</span><span class="p">:</span><span class="w"> </span><span class="l">separator</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="w"> </span><span class="nt">weight</span><span class="p">:</span><span class="w"> </span><span class="m">1</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="w"> </span>- <span class="nt">name</span><span class="p">:</span><span class="w"> </span><span class="s2">"A page"</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="w"> </span><span class="nt">pageRef</span><span class="p">:</span><span class="w"> </span><span class="s2">"/page-filename-here"</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="w"> </span><span class="nt">weight</span><span class="p">:</span><span class="w"> </span><span class="m">2</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="w"> </span>- <span class="nt">name</span><span class="p">:</span><span class="w"> </span><span class="s2">"An external link ↗"</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="w"> </span><span class="nt">url</span><span class="p">:</span><span class="w"> </span><span class="s2">"https://hugoblox.com"</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="w"> </span><span class="nt">weight</span><span class="p">:</span><span class="w"> </span><span class="m">3</span><span class="w"> </span></span></span></code></pre></div><h2 id="right-sidebar">Right Sidebar</h2> <p>A table of contents is automatically generated from the headings your Markdown file.</p> <p>It can optionally be disabled by setting <code>toc: false</code> in the front matter of a page:</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-yaml" data-lang="yaml"><span class="line"><span class="cl"><span class="nn">---</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="nt">title</span><span class="p">:</span><span class="w"> </span><span class="l">My Page</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="nt">toc</span><span class="p">:</span><span class="w"> </span><span class="kc">false</span><span class="w"> </span></span></span><span class="line"><span class="cl"><span class="nn">---</span><span class="w"> </span></span></span></code></pre></div> </article> <article> <h1>A new review on spatial cell-cell communication analysis</h1> <p>Fri, 21 Aug 2026 00:00:00 +0000</p> </article> <article> <h1>Prediction of single cell gene expression</h1> <p>Fri, 21 Aug 2026 00:00:00 +0000</p> <p>Learning the relationship between gene-regulatory regions from epigenome and transcriptome data measured for single-cell is hard. We have developed an automated Nextflow pipeline that addresses the noise and sparsity of single-cell data by aggregating individual cells into metacells. We show that analysis on metacell level often leads to superior models and we illustrate the use of these models on different datasets.</p> <div class="cite-list"> <h2>Linked publications</h2> <div class="pub-list-item view-citation" style="margin-bottom: 1rem"> <i class="far fa-file-alt pub-icon" aria-hidden="true"></i> <span class="article-metadata li-cite-author"> <span ><a href="">Laura Rumpf</a></span>, <span ><a href="">Fatemeh Behjati Ardakani</a></span>, <span ><a href="">Dennis Hecker</a></span>, <span ><a href="">Marcel H. Schulz</a></span> </span> (2026). <a href="https://cgm.uni-frankfurt.de/publications/rumpf-predicting-2026/" class="underline">Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data</a>. <em>Bioinformatics</em>. <div class="flex flex-wrap space-x-3"> <button class="hb-attachment-link hb-attachment-link-small js-cite-clipboard cursor-pointer" type="button" data-filename="/publications/rumpf-predicting-2026/cite.bib"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M15.75 17.25v3.375c0 .621-.504 1.125-1.125 1.125h-9.75a1.125 1.125 0 0 1-1.125-1.125V7.875c0-.621.504-1.125 1.125-1.125H6.75a9 9 0 0 1 1.5.124m7.5 10.376h3.375c.621 0 1.125-.504 1.125-1.125V11.25c0-4.46-3.243-8.161-7.5-8.876a9 9 0 0 0-1.5-.124H9.375c-.621 0-1.125.504-1.125 1.125v3.5m7.5 10.375H9.375a1.125 1.125 0 0 1-1.125-1.125v-9.25m12 6.625v-1.875a3.375 3.375 0 0 0-3.375-3.375h-1.5a1.125 1.125 0 0 1-1.125-1.125v-1.5a3.375 3.375 0 0 0-3.375-3.375H9.75"/></svg> <span>Cite</span> </button> <a class="hb-attachment-link hb-attachment-link-small" href="https://doi.org/10.1093/bioinformatics/btag299" target="_blank" rel="noopener"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.19 8.688a4.5 4.5 0 0 1 1.242 7.244l-4.5 4.5a4.5 4.5 0 0 1-6.364-6.364l1.757-1.757m13.35-.622l1.757-1.757a4.5 4.5 0 0 0-6.364-6.364l-4.5 4.5a4.5 4.5 0 0 0 1.242 7.244"/></svg> DOI </a> </div> </div> </div> </article> <article> <h1>Incorporating deep learning TF models into SNEEP</h1> <p>Thu, 13 Aug 2026 00:00:00 +0000</p> <h2 id="project-description">Project Description</h2> <p>In our lab, we developed a statistical approach (SNEEP, see ) that identifies regulatory single nucleotide variants (SNVs) affecting transcription factor (TF) binding. Currently, the approach uses position weight matrices (PWMs) as TF models. However, these models have disadvantages, and the community has been investigating more reliable models based on deep learning, such as BPNet. Recently, the TF database JASPAR extended its set of available motifs by adding a large collection of TF-specific BPNet models, which can be used as an alternative to the classical PWM approach.</p> <p>This project focuses on improving and adapting our SNEEP approach by incorporating these deep learning models as TF models.</p> <h2 id="research-goals">Research Goals</h2> <ul> <li>Explore how to derive a differential TF binding score and p-value using BPNet models per TF. Investigate whether the SNEEP statistic is still applicable. If not, figure out which changes need to be made.</li> <li>Analyze how deletions and insertions can be handled</li> <li>Adapt the SNEEP software accordingly</li> <li>Test the new implementation</li> <li>Evaluate and compare the results to the previous version of SNEEP</li> </ul> <h2 id="prerequisites">Prerequisites</h2> <ul> <li>C++ programming or motivation to learn it</li> <li>Basic knowlegde of genomics is helpful, but not required</li> </ul> <h2 id="how-to-apply">How to Apply</h2> <p>Send an Email with a short motivation to the corresponding supervisor .</p> </article> <article> <h1>Modifying SNEEP to account for averaged differential TF Binding</h1> <p>Thu, 13 Aug 2026 00:00:00 +0000</p> <h2 id="project-description">Project Description</h2> <p>In our lab, we developed a statistical approach (SNEEP, see ) that identifies regulatory single nucleotide variants (SNVs) affecting transcription factor (TF) binding. Currently, the approach uses a maximization to identify the position with the strongest differential TF binding score. However, recent studies show that TFs might also bind at sites where several medium-strength binding sites overlap.</p> <p>This project focuses on improving and adapting our SNEEP approach by modifying the underlying statistical model such that the above-described binding behavior is taken into account.</p> <h2 id="research-goals">Research Goals</h2> <ul> <li>Modify the SNEEP statistic to use an average differential TF binding score instead of the maximum</li> <li>Adapt the SNEEP software accordingly</li> <li>Test the new implementation</li> <li>Evaluate and compare the results to the previous version of SNEEP</li> </ul> <h2 id="prerequisites">Prerequisites</h2> <ul> <li>C++ programming or motivation to learn it</li> <li>Basic knowlegde of genomics is helpful, but not required</li> </ul> <h2 id="how-to-apply">How to Apply</h2> <p>Send an Email with a short motivation to the corresponding supervisor .</p> </article> <article> <h1>Placing regulatory variants into tissue context</h1> <p>Wed, 12 Aug 2026 00:00:00 +0000</p> <h2 id="project-description">Project Description</h2> <p>With the rapid development of spatial transcriptomics techniques, the bioinformatics possibilities in this research area are growing as well. A recent approach (gsMAP) integrates spatial transcriptomics data with genome-wide association study (GWAS) summary statistics, enabling spatially resolved linking of genetic associations to individual cells.</p> <p>In our lab, we developed a statistical approach (SNEEP, see ) that identifies regulatory single nucleotide variants that impact transcription factor binding in cis-regulatory elements, such as enhancer. This project aims to incorporate SNEEP into gsMAP in order to improve the inclusion of functionally important regulatory variants to the spatial mapping step.</p> <h2 id="research-goals">Research Goals</h2> <ul> <li>Combine SNEEP and gsMAP</li> <li>Test the new implementation</li> <li>Evaluate and compare the results to the original method</li> </ul> <h2 id="prerequisites">Prerequisites</h2> <ul> <li>Python programming</li> <li>Basic knowlegde of genomics is helpful, but not required</li> </ul> <h2 id="how-to-apply">How to Apply</h2> <p>Send an Email with a short motivation to the corresponding supervisor .</p> </article> <article> <h1>A categorization of spatial transcriptomics methods for cell–cell communication analysis</h1> <p>Sat, 01 Aug 2026 00:00:00 +0000</p> </article> <article> <h1>MOPRED Symposium 2026</h1> <p>Wed, 29 Jul 2026 00:00:00 +0000</p> <p>Hugo Blox is designed to give technical content creators a seamless experience. 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my-6" role="article" aria-labelledby="hb-embed-title-hb-embed-0b44c90afbe72f85feebf4a6af743d72"> <div class="flex items-center gap-3 p-6 border-b border-zinc-100 dark:border-zinc-800"> <div class="flex-shrink-0"> <div class="w-10 h-10 rounded-full bg-gradient-to-br from-yellow-400 to-orange-500 flex items-center justify-center"> <svg class="w-6 h-6 text-white" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="currentColor" d="M12.025 1.13c-5.77 0-10.449 4.647-10.449 10.378c0 1.112.178 2.181.503 3.185c.064-.222.203-.444.416-.577a.96.96 0 0 1 .524-.15c.293 0 .584.124.84.284c.278.173.48.408.71.694c.226.282.458.611.684.951v-.014c.017-.324.106-.622.264-.874s.403-.487.762-.543c.3-.047.596.06.787.203s.31.313.4.467c.15.257.212.468.233.542c.01.026.653 1.552 1.657 2.54c.616.605 1.01 1.223 1.082 1.912c.055.537-.096 1.059-.38 1.572c.637.121 1.294.187 1.967.187c.657 0 1.298-.063 1.921-.178c-.287-.517-.44-1.041-.384-1.581c.07-.69.465-1.307 1.081-1.913c1.004-.987 1.647-2.513 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rounded-full bg-primary-500"></span> <span class="text-sm text-zinc-600 dark:text-zinc-400 capitalize"> dataset </span></div> </div> <div class="flex-shrink-0"> <a href="https://huggingface.co/datasets/fka/awesome-chatgpt-prompts" target="_blank" rel="noopener" class="text-zinc-400 hover:text-primary-500 transition-colors duration-200"> <svg class="w-5 h-5 hb-embed-link" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.5 6H5.25A2.25 2.25 0 0 0 3 8.25v10.5A2.25 2.25 0 0 0 5.25 21h10.5A2.25 2.25 0 0 0 18 18.75V10.5m-10.5 6L21 3m0 0h-5.25M21 3v5.25"/></svg> </a> </div> </div> <div class="p-6 space-y-4"> <p class="text-zinc-600 dark:text-zinc-400 text-base leading-relaxed line-clamp-3"> a.k.a. Awesome ChatGPT Prompts This is a Dataset Repository mirror of prompts.chat — a social platform for AI prompts. 📢 Notice This Hugging Face dataset is a mirror. For the … </p><div class="flex items-center gap-6 pt-2"><div class="flex items-center gap-1.5 text-sm text-zinc-600 dark:text-zinc-400"> <svg class="w-4 h-4 text-primary-500" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M3 16.5v2.25A2.25 2.25 0 0 0 5.25 21h13.5A2.25 2.25 0 0 0 21 18.75V16.5M16.5 12L12 16.5m0 0L7.5 12m4.5 4.5V3"/></svg><span id="hb-hb-embed-0b44c90afbe72f85feebf4a6af743d72-downloads">31.596k</span></div><div class="flex items-center gap-1.5 text-sm text-zinc-600 dark:text-zinc-400"> <svg class="w-4 h-4 text-secondary-500" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M21 8.25c0-2.485-2.099-4.5-4.687-4.5c-1.936 0-3.598 1.126-4.313 2.733c-.715-1.607-2.377-2.733-4.312-2.733C5.098 3.75 3 5.765 3 8.25c0 7.22 9 12 9 12s9-4.78 9-12"/></svg><span id="hb-hb-embed-0b44c90afbe72f85feebf4a6af743d72-likes">9.745k</span></div></div> </div> <div class="absolute inset-0 pointer-events-none bg-gradient-to-r from-primary-500/0 via-primary-500/5 to-secondary-500/0 opacity-0 group-hover:opacity-100 transition-opacity duration-300"></div> <div class="sr-only" data-hb-component="embed" data-hb-version="1.0" data-hb-license="MIT"> Powered by Hugo Blox Kit - https://github.com/HugoBlox/kit </div> </div> <p>GitHub Repository</p> <div class="group bg-white/90 dark:bg-zinc-900/90 backdrop-blur-sm rounded-2xl ring-1 ring-zinc-900/5 dark:ring-white/10 shadow-lg overflow-hidden transition-all duration-300 ease-out hover:shadow-xl hover:shadow-primary-500/10 hover:-translate-y-1 focus-within:ring-2 focus-within:ring-primary-500/50 my-6" role="article" aria-labelledby="hb-embed-title-hb-embed-63c24024d739b03e5a3e807f5e2314ab"> <div class="flex items-center gap-3 p-6 border-b border-zinc-100 dark:border-zinc-800"> <div class="flex-shrink-0"> <div class="w-10 h-10 rounded-full bg-gradient-to-br from-slate-800 to-slate-900 flex items-center justify-center"> <svg class="w-6 h-6 text-white" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="currentColor" d="M12 .297c-6.63 0-12 5.373-12 12c0 5.303 3.438 9.8 8.205 11.385c.6.113.82-.258.82-.577c0-.285-.01-1.04-.015-2.04c-3.338.724-4.042-1.61-4.042-1.61C4.422 18.07 3.633 17.7 3.633 17.7c-1.087-.744.084-.729.084-.729c1.205.084 1.838 1.236 1.838 1.236c1.07 1.835 2.809 1.305 3.495.998c.108-.776.417-1.305.76-1.605c-2.665-.3-5.466-1.332-5.466-5.93c0-1.31.465-2.38 1.235-3.22c-.135-.303-.54-1.523.105-3.176c0 0 1.005-.322 3.3 1.23c.96-.267 1.98-.399 3-.405c1.02.006 2.04.138 3 .405c2.28-1.552 3.285-1.23 3.285-1.23c.645 1.653.24 2.873.12 3.176c.765.84 1.23 1.91 1.23 3.22c0 4.61-2.805 5.625-5.475 5.92c.42.36.81 1.096.81 2.22c0 1.606-.015 2.896-.015 3.286c0 .315.21.69.825.57C20.565 22.092 24 17.592 24 12.297c0-6.627-5.373-12-12-12"/></svg> </div> </div> <div class="flex-1 min-w-0"> <h3 id="hb-embed-title-hb-embed-63c24024d739b03e5a3e807f5e2314ab" class="text-xl font-bold tracking-tight leading-tight truncate"> <a href="https://github.com/HugoBlox/kit" target="_blank" rel="noopener" class="text-zinc-900 dark:text-zinc-100 hover:text-primary-600 dark:hover:text-primary-400 hover:underline transition-colors duration-200">kit</a> </h3> <div class="flex items-center gap-2 mt-1"> <span class="text-sm text-zinc-600 dark:text-zinc-400">by <a href="https://github.com/HugoBlox" target="_blank" rel="noopener" class="font-medium hover:text-primary-600 dark:hover:text-primary-400 hover:underline transition-colors duration-200">HugoBlox</a> </span><span class="text-sm text-zinc-500 dark:text-zinc-500">•</span> <span class="inline-block w-2 h-2 rounded-full bg-primary-500"></span> <span class="text-sm text-zinc-500 dark:text-zinc-500 capitalize">HTML</span></div> </div> <div class="flex-shrink-0"> <a href="https://github.com/HugoBlox/kit" target="_blank" rel="noopener" class="text-zinc-400 hover:text-primary-500 transition-colors duration-200"> <svg class="w-5 h-5 hb-embed-link" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.5 6H5.25A2.25 2.25 0 0 0 3 8.25v10.5A2.25 2.25 0 0 0 5.25 21h10.5A2.25 2.25 0 0 0 18 18.75V10.5m-10.5 6L21 3m0 0h-5.25M21 3v5.25"/></svg> </a> </div> </div> <div class="p-6 space-y-4"> <p class="text-zinc-600 dark:text-zinc-400 text-base leading-relaxed line-clamp-3"> 🧱 Describe your site, AI builds it, you own it as Markdown. Snap together Tailwind blocks like Lego — landing pages, blogs, portfolios, docs & more. No AI slop. Free to deploy anywhere 👇 </p><div class="flex items-center gap-6 pt-2"><div class="flex items-center gap-1.5 text-sm text-zinc-600 dark:text-zinc-400"> <svg class="w-4 h-4 text-primary-500" xmlns="http://www.w3.org/2000/svg" fill="currentColor" viewBox="0 0 24 24"><path d="M6 2C4.89543 2 4 2.89543 4 4C4 4.74028 4.4022 5.38663 5 5.73244V7C5 8.65685 6.34315 10 8 10H10V11.2676C9.4022 11.6134 9 12.2597 9 13C9 14.1046 9.89543 15 11 15C12.1046 15 13 14.1046 13 13C13 12.2597 12.5978 11.6134 12 11.2676V10H14C15.6569 10 17 8.65685 17 7V5.73244C17.5978 5.38663 18 4.74028 18 4C18 2.89543 17.1046 2 16 2C14.8954 2 14 2.89543 14 4C14 4.74028 14.4022 5.38663 15 5.73244V7C15 7.55228 14.5523 8 14 8H8C7.44772 8 7 7.55228 7 7V5.73244C7.5978 5.38663 8 4.74028 8 4C8 2.89543 7.10457 2 6 2ZM6 4C6 3.44772 6.44772 3 7 3C7.55228 3 8 3.44772 8 4C8 4.55228 7.55228 5 7 5C6.44772 5 6 4.55228 6 4ZM11 13C11 12.4477 11.4477 12 12 12C12.5523 12 13 12.4477 13 13C13 13.5523 12.5523 14 12 14C11.4477 14 11 13.5523 11 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id="hb-embed-title-hb-embed-95aff9f9d03b52cfc929778015aed047" class="text-xl font-bold tracking-tight leading-tight truncate"> <a href="https://example.com" target="_blank" rel="noopener" class="text-zinc-900 dark:text-zinc-100 hover:text-primary-600 dark:hover:text-primary-400 hover:underline transition-colors duration-200">My Custom Resource</a> </h3> <div class="flex items-center gap-2 mt-1"> <span class="text-sm text-zinc-500 dark:text-zinc-500">example.com</span></div> </div> <div class="flex-shrink-0"> <a href="https://example.com" target="_blank" rel="noopener" class="text-zinc-400 hover:text-primary-500 transition-colors duration-200"> <svg class="w-5 h-5 hb-embed-link" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.5 6H5.25A2.25 2.25 0 0 0 3 8.25v10.5A2.25 2.25 0 0 0 5.25 21h10.5A2.25 2.25 0 0 0 18 18.75V10.5m-10.5 6L21 3m0 0h-5.25M21 3v5.25"/></svg> </a> </div> </div> <div class="p-6 space-y-4"> <p class="text-zinc-600 dark:text-zinc-400 text-base leading-relaxed line-clamp-3"> A great resource for learning </p> </div> <div class="absolute inset-0 pointer-events-none bg-gradient-to-r from-primary-500/0 via-primary-500/5 to-secondary-500/0 opacity-0 group-hover:opacity-100 transition-opacity duration-300"></div> <div class="sr-only" data-hb-component="embed" data-hb-version="1.0" data-hb-license="MIT"> Powered by Hugo Blox Kit - https://github.com/HugoBlox/kit </div> </div> <h3 id="custom-images">Custom Images</h3> <p>Embed beautiful images from any source with Hugo image processing (Unsplash, custom URLs, etc.):</p> <div class="group bg-white/90 dark:bg-zinc-900/90 backdrop-blur-sm rounded-2xl ring-1 ring-zinc-900/5 dark:ring-white/10 shadow-lg overflow-hidden transition-all duration-300 ease-out hover:shadow-xl hover:shadow-primary-500/10 hover:-translate-y-1 focus-within:ring-2 focus-within:ring-primary-500/50 my-6" role="article" aria-labelledby="hb-embed-title-hb-embed-7fb8d015167a99890a4bddfec03ca297"> <div class="flex items-center gap-3 p-6 border-b border-zinc-100 dark:border-zinc-800"> <div class="flex-shrink-0"> <div class="w-10 h-10 rounded-full bg-gradient-to-br from-zinc-700 to-zinc-800 flex items-center justify-center"> <svg class="w-5 h-5 text-white" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M12 21a9.004 9.004 0 0 0 8.716-6.747M12 21a9.004 9.004 0 0 1-8.716-6.747M12 21c2.485 0 4.5-4.03 4.5-9S14.485 3 12 3m0 18c-2.485 0-4.5-4.03-4.5-9S9.515 3 12 3m0 0a9 9 0 0 1 7.843 4.582M12 3a9 9 0 0 0-7.843 4.582m15.686 0A11.95 11.95 0 0 1 12 10.5c-2.998 0-5.74-1.1-7.843-2.918m15.686 0A8.96 8.96 0 0 1 21 12c0 .778-.099 1.533-.284 2.253m0 0A17.9 17.9 0 0 1 12 16.5a17.9 17.9 0 0 1-8.716-2.247m0 0A9 9 0 0 1 3 12c0-1.605.42-3.113 1.157-4.418"/></svg> </div> </div> <div class="flex-1 min-w-0"> <h3 id="hb-embed-title-hb-embed-7fb8d015167a99890a4bddfec03ca297" class="text-xl font-bold tracking-tight leading-tight truncate"> <a href="https://example.com" target="_blank" rel="noopener" class="text-zinc-900 dark:text-zinc-100 hover:text-primary-600 dark:hover:text-primary-400 hover:underline transition-colors duration-200">Data Visualization Guide</a> </h3> <div class="flex items-center gap-2 mt-1"> <span class="text-sm text-zinc-500 dark:text-zinc-500">example.com</span></div> </div> <div class="flex-shrink-0"> <a href="https://example.com" target="_blank" rel="noopener" class="text-zinc-400 hover:text-primary-500 transition-colors duration-200"> <svg class="w-5 h-5 hb-embed-link" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.5 6H5.25A2.25 2.25 0 0 0 3 8.25v10.5A2.25 2.25 0 0 0 5.25 21h10.5A2.25 2.25 0 0 0 18 18.75V10.5m-10.5 6L21 3m0 0h-5.25M21 3v5.25"/></svg> </a> </div> </div> <div class="p-6 space-y-4"> <div class="mb-4 overflow-hidden rounded-lg"> </div><p class="text-zinc-600 dark:text-zinc-400 text-base leading-relaxed line-clamp-3"> Beautiful data visualization workspace </p> </div> <div class="absolute inset-0 pointer-events-none bg-gradient-to-r from-primary-500/0 via-primary-500/5 to-secondary-500/0 opacity-0 group-hover:opacity-100 transition-opacity duration-300"></div> <div class="sr-only" data-hb-component="embed" data-hb-version="1.0" data-hb-license="MIT"> Powered by Hugo Blox Kit - https://github.com/HugoBlox/kit </div> </div> <p>You can also add images to any platform embed:</p> <div class="group bg-white/90 dark:bg-zinc-900/90 backdrop-blur-sm rounded-2xl ring-1 ring-zinc-900/5 dark:ring-white/10 shadow-lg overflow-hidden transition-all duration-300 ease-out hover:shadow-xl hover:shadow-primary-500/10 hover:-translate-y-1 focus-within:ring-2 focus-within:ring-primary-500/50 my-6" role="article" aria-labelledby="hb-embed-title-hb-embed-f4e6971e1a47a6dcd2db11bcdbad3df8"> <div class="flex items-center gap-3 p-6 border-b border-zinc-100 dark:border-zinc-800"> <div class="flex-shrink-0"> <div class="w-10 h-10 rounded-full bg-gradient-to-br from-slate-800 to-slate-900 flex items-center justify-center"> <svg class="w-6 h-6 text-white" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="currentColor" d="M12 .297c-6.63 0-12 5.373-12 12c0 5.303 3.438 9.8 8.205 11.385c.6.113.82-.258.82-.577c0-.285-.01-1.04-.015-2.04c-3.338.724-4.042-1.61-4.042-1.61C4.422 18.07 3.633 17.7 3.633 17.7c-1.087-.744.084-.729.084-.729c1.205.084 1.838 1.236 1.838 1.236c1.07 1.835 2.809 1.305 3.495.998c.108-.776.417-1.305.76-1.605c-2.665-.3-5.466-1.332-5.466-5.93c0-1.31.465-2.38 1.235-3.22c-.135-.303-.54-1.523.105-3.176c0 0 1.005-.322 3.3 1.23c.96-.267 1.98-.399 3-.405c1.02.006 2.04.138 3 .405c2.28-1.552 3.285-1.23 3.285-1.23c.645 1.653.24 2.873.12 3.176c.765.84 1.23 1.91 1.23 3.22c0 4.61-2.805 5.625-5.475 5.92c.42.36.81 1.096.81 2.22c0 1.606-.015 2.896-.015 3.286c0 .315.21.69.825.57C20.565 22.092 24 17.592 24 12.297c0-6.627-5.373-12-12-12"/></svg> </div> </div> <div class="flex-1 min-w-0"> <h3 id="hb-embed-title-hb-embed-f4e6971e1a47a6dcd2db11bcdbad3df8" class="text-xl font-bold tracking-tight leading-tight truncate"> <a href="https://github.com/plotly/plotly.py" target="_blank" rel="noopener" class="text-zinc-900 dark:text-zinc-100 hover:text-primary-600 dark:hover:text-primary-400 hover:underline transition-colors duration-200">plotly.py</a> </h3> <div class="flex items-center gap-2 mt-1"> <span class="text-sm text-zinc-600 dark:text-zinc-400">by <a href="https://github.com/plotly" target="_blank" rel="noopener" class="font-medium hover:text-primary-600 dark:hover:text-primary-400 hover:underline transition-colors duration-200">plotly</a> </span><span class="text-sm text-zinc-500 dark:text-zinc-500">•</span> <span class="inline-block w-2 h-2 rounded-full bg-primary-500"></span> <span class="text-sm text-zinc-500 dark:text-zinc-500 capitalize">Python</span></div> </div> <div class="flex-shrink-0"> <a href="https://github.com/plotly/plotly.py" target="_blank" rel="noopener" class="text-zinc-400 hover:text-primary-500 transition-colors duration-200"> <svg class="w-5 h-5 hb-embed-link" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.5 6H5.25A2.25 2.25 0 0 0 3 8.25v10.5A2.25 2.25 0 0 0 5.25 21h10.5A2.25 2.25 0 0 0 18 18.75V10.5m-10.5 6L21 3m0 0h-5.25M21 3v5.25"/></svg> </a> </div> </div> <div class="p-6 space-y-4"> <div class="mb-4 overflow-hidden rounded-lg"> </div><p class="text-zinc-600 dark:text-zinc-400 text-base leading-relaxed line-clamp-3"> The interactive graphing library for Python ✨ </p><div class="flex items-center gap-6 pt-2"><div class="flex items-center gap-1.5 text-sm text-zinc-600 dark:text-zinc-400"> <svg class="w-4 h-4 text-primary-500" xmlns="http://www.w3.org/2000/svg" fill="currentColor" viewBox="0 0 24 24"><path d="M6 2C4.89543 2 4 2.89543 4 4C4 4.74028 4.4022 5.38663 5 5.73244V7C5 8.65685 6.34315 10 8 10H10V11.2676C9.4022 11.6134 9 12.2597 9 13C9 14.1046 9.89543 15 11 15C12.1046 15 13 14.1046 13 13C13 12.2597 12.5978 11.6134 12 11.2676V10H14C15.6569 10 17 8.65685 17 7V5.73244C17.5978 5.38663 18 4.74028 18 4C18 2.89543 17.1046 2 16 2C14.8954 2 14 2.89543 14 4C14 4.74028 14.4022 5.38663 15 5.73244V7C15 7.55228 14.5523 8 14 8H8C7.44772 8 7 7.55228 7 7V5.73244C7.5978 5.38663 8 4.74028 8 4C8 2.89543 7.10457 2 6 2ZM6 4C6 3.44772 6.44772 3 7 3C7.55228 3 8 3.44772 8 4C8 4.55228 7.55228 5 7 5C6.44772 5 6 4.55228 6 4ZM11 13C11 12.4477 11.4477 12 12 12C12.5523 12 13 12.4477 13 13C13 13.5523 12.5523 14 12 14C11.4477 14 11 13.5523 11 13ZM16 3C15.4477 3 15 3.44772 15 4C15 4.55228 15.4477 5 16 5C16.5523 5 17 4.55228 17 4C17 3.44772 16.5523 3 16 3Z"/></svg><span id="hb-hb-embed-f4e6971e1a47a6dcd2db11bcdbad3df8-forks">2.815k</span></div><div class="flex items-center gap-1.5 text-sm text-zinc-600 dark:text-zinc-400"> <svg class="w-4 h-4 text-red-500" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M12 9v3.75m9-.75a9 9 0 1 1-18 0a9 9 0 0 1 18 0m-9 3.75h.008v.008H12z"/></svg> <a href="https://github.com/plotly/plotly.py/issues" target="_blank" rel="noopener" class="font-medium hover:text-primary-600 dark:hover:text-primary-400 hover:underline transition-colors duration-200" id="hb-hb-embed-f4e6971e1a47a6dcd2db11bcdbad3df8-issues">768</a></div><div class="flex items-center gap-1.5 text-sm text-zinc-600 dark:text-zinc-400"> <svg class="w-4 h-4 text-yellow-500" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M11.48 3.499a.562.562 0 0 1 1.04 0l2.125 5.111a.56.56 0 0 0 .475.345l5.518.442c.499.04.701.663.321.988l-4.204 3.602a.56.56 0 0 0-.182.557l1.285 5.385a.562.562 0 0 1-.84.61l-4.725-2.885a.56.56 0 0 0-.586 0L6.982 20.54a.562.562 0 0 1-.84-.61l1.285-5.386a.56.56 0 0 0-.182-.557l-4.204-3.602a.562.562 0 0 1 .321-.988l5.518-.442a.56.56 0 0 0 .475-.345z"/></svg><span id="hb-hb-embed-f4e6971e1a47a6dcd2db11bcdbad3df8-stars">18.631k</span></div></div><div class="flex flex-wrap gap-1 pt-2"><span class="inline-flex items-center px-2 py-0.5 rounded-full text-xs font-medium bg-primary-100 text-primary-800 dark:bg-primary-900/40 dark:text-primary-300"> d3 </span><span class="inline-flex items-center px-2 py-0.5 rounded-full text-xs font-medium bg-primary-100 text-primary-800 dark:bg-primary-900/40 dark:text-primary-300"> dashboard </span><span class="inline-flex items-center px-2 py-0.5 rounded-full text-xs font-medium bg-primary-100 text-primary-800 dark:bg-primary-900/40 dark:text-primary-300"> declarative </span><span class="text-xs text-zinc-500 dark:text-zinc-500">+11</span></div> </div> <div class="absolute inset-0 pointer-events-none bg-gradient-to-r from-primary-500/0 via-primary-500/5 to-secondary-500/0 opacity-0 group-hover:opacity-100 transition-opacity duration-300"></div> <div class="sr-only" data-hb-component="embed" data-hb-version="1.0" data-hb-license="MIT"> Powered by Hugo Blox Kit - https://github.com/HugoBlox/kit </div> </div> <h2 id="charts">Charts</h2> <p>Hugo Blox supports the popular format for interactive data visualizations. With Plotly, you can design almost any kind of visualization you can imagine!</p> <p>Save your Plotly JSON in your page folder, for example <code>line-chart.json</code>, and then add the <code>{{< chart data="line-chart" >}}</code> shortcode where you would like the chart to appear.</p> <p>Demo:</p> <div id="chart-361859742" class="chart"></div> <script> (function() { async function fetchChartJSON() { console.debug('Hugo Blox fetching chart JSON...') const response = await fetch('.\/line-chart.json'); return await response.json(); } let a = setInterval( function() { if ( typeof window.Plotly === 'undefined' ) { console.debug('Plotly not loaded yet...') return; } clearInterval( a ); fetchChartJSON().then(chart => { console.debug('Plotting chart...') window.Plotly.newPlot('chart-361859742', chart.data, chart.layout, {responsive: true}); }); }, 500 ); })(); </script> <p>You might also find the useful.</p> <h2 id="diagrams">Diagrams</h2> <p>Hugo Blox supports the <em>Mermaid</em> Markdown extension for diagrams.</p> <p>An example <strong>flowchart</strong>:</p> <pre><code>```mermaid graph TD A[Hard] -->|Text| B(Round) B --> C{Decision} C -->|One| D[Result 1] C -->|Two| E[Result 2] ``` </code></pre> <p>renders as</p> <div class="mermaid">graph TD A[Hard] -->|Text| B(Round) B --> C{Decision} C -->|One| D[Result 1] C -->|Two| E[Result 2] </div> <p>An example <strong>sequence diagram</strong>:</p> <pre><code>```mermaid sequenceDiagram Alice->>John: Hello John, how are you? loop Healthcheck John->>John: Fight against hypochondria end Note right of John: Rational thoughts! John-->>Alice: Great! John->>Bob: How about you? Bob-->>John: Jolly good! ``` </code></pre> <p>renders as</p> <div class="mermaid">sequenceDiagram Alice->>John: Hello John, how are you? loop Healthcheck John->>John: Fight against hypochondria end Note right of John: Rational thoughts! John-->>Alice: Great! John->>Bob: How about you? Bob-->>John: Jolly good! </div> <p>An example <strong>class diagram</strong>:</p> <pre><code>```mermaid classDiagram Class01 <|-- AveryLongClass : Cool Class03 *-- Class04 Class05 o-- Class06 Class07 .. Class08 Class09 --> C2 : Where am i? Class09 --* C3 Class09 --|> Class07 Class07 : equals() Class07 : Object[] elementData Class01 : size() Class01 : int chimp Class01 : int gorilla Class08 <--> C2: Cool label ``` </code></pre> <p>renders as</p> <div class="mermaid">classDiagram Class01 <|-- AveryLongClass : Cool Class03 *-- Class04 Class05 o-- Class06 Class07 .. Class08 Class09 --> C2 : Where am i? Class09 --* C3 Class09 --|> Class07 Class07 : equals() Class07 : Object[] elementData Class01 : size() Class01 : int chimp Class01 : int gorilla Class08 <--> C2: Cool label </div> <p>An example <strong>state diagram</strong>:</p> <pre><code>```mermaid stateDiagram [*] --> Still Still --> [*] Still --> Moving Moving --> Still Moving --> Crash Crash --> [*] ``` </code></pre> <p>renders as</p> <div class="mermaid">stateDiagram [*] --> Still Still --> [*] Still --> Moving Moving --> Still Moving --> Crash Crash --> [*] </div> <h2 id="data-frames">Data Frames</h2> <p>Save your spreadsheet as a CSV file in your page’s folder and then render it by adding the <em>Table</em> shortcode to your page:</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go" data-lang="go"><span class="line"><span class="cl"><span class="p">{{<</span><span class="w"> </span><span class="nx">table</span><span class="w"> </span><span class="nx">path</span><span class="p">=</span><span class="s">"results.csv"</span><span class="w"> </span><span class="nx">header</span><span class="p">=</span><span class="s">"true"</span><span class="w"> </span><span class="nx">caption</span><span class="p">=</span><span class="s">"Table 1: My results"</span><span class="w"> </span><span class="p">>}}</span><span class="w"> </span></span></span></code></pre></div><p>renders as</p> <table class="table-auto w-full"> <thead> <tr> <th class="border-b dark:border-slate-600 font-medium p-4 pt-0 pb-3 text-slate-400 dark:text-slate-200 text-left">customer_id</th> <th class="border-b dark:border-slate-600 font-medium p-4 pt-0 pb-3 text-slate-400 dark:text-slate-200 text-left">score</th> </tr> </thead> <tbody> <tr> <td data-table-dtype="number" class="border-b border-slate-100 dark:border-slate-700 p-4 text-slate-500 dark:text-slate-400">1</td> <td data-table-dtype="number" class="border-b border-slate-100 dark:border-slate-700 p-4 text-slate-500 dark:text-slate-400">0</td> </tr> <tr> <td data-table-dtype="number" class="border-b border-slate-100 dark:border-slate-700 p-4 text-slate-500 dark:text-slate-400">2</td> <td data-table-dtype="text" class="border-b border-slate-100 dark:border-slate-700 p-4 text-slate-500 dark:text-slate-400">0.5</td> </tr> <tr> <td data-table-dtype="number" class="border-b border-slate-100 dark:border-slate-700 p-4 text-slate-500 dark:text-slate-400">3</td> <td data-table-dtype="number" class="border-b border-slate-100 dark:border-slate-700 p-4 text-slate-500 dark:text-slate-400">1</td> </tr> </tbody> <caption class="table-caption">Table 1: My results</caption> </table> <h2 id="interactive-buttons">Interactive Buttons</h2> <p>Add engaging call-to-action buttons to your data visualization posts:</p> <h3 id="basic-buttons">Basic Buttons</h3> <div class="text-left"> <a id="button-dc6c8213a600c6eea5a517fb17bde3c7" href="https://cgm.uni-frankfurt.de/" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Contact Us" > <span>Contact Us</span> </a> </div> <p> </p> <div class="text-left"> <a id="button-b2cd26f5e86920fd45f39bf7cdff0b77" href="https://plotly.com/python/" target="_blank" rel="noopener noreferrer" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-secondary-500 to-secondary-600 hover:from-secondary-600 hover:to-secondary-700 active:from-secondary-700 active:to-secondary-800 text-white shadow-lg shadow-secondary-500/25 hover:shadow-xl hover:shadow-secondary-500/30 hover:scale-105 active:scale-95 focus:ring-secondary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Learn Plotly" > <span>Learn Plotly</span> </a> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"/"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Contact Us<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"https://plotly.com/python/"</span><span class="w"> </span><span class="nx">new_tab</span><span class="o">=</span><span class="s">"true"</span><span class="w"> </span><span class="nx">style</span><span class="o">=</span><span class="s">"secondary"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Learn Plotly<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h3 id="styled-buttons-for-data-actions">Styled Buttons for Data Actions</h3> <div class="text-center"> <a id="button-a9be86601f215b9cb8b7275313561810" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-6 py-3 text-lg rounded-lg" role="button" aria-label="View Dashboard" > <span class="flex-shrink-0"> <svg class="w-4 h-4" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M3 13.125C3 12.504 3.504 12 4.125 12h2.25c.621 0 1.125.504 1.125 1.125v6.75C7.5 20.496 6.996 21 6.375 21h-2.25A1.125 1.125 0 0 1 3 19.875zm6.75-4.5c0-.621.504-1.125 1.125-1.125h2.25c.621 0 1.125.504 1.125 1.125v11.25c0 .621-.504 1.125-1.125 1.125h-2.25a1.125 1.125 0 0 1-1.125-1.125zm6.75-4.5c0-.621.504-1.125 1.125-1.125h2.25C20.496 3 21 3.504 21 4.125v15.75c0 .621-.504 1.125-1.125 1.125h-2.25a1.125 1.125 0 0 1-1.125-1.125z"/></svg> </span> <span>View Dashboard</span> </a> </div> <p> </p> <div class="text-left"> <a id="button-7022937617e6161bde01e5fa137b06fb" href="https://cgm.uni-frankfurt.de/data/results.csv" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-white dark:bg-zinc-900 border-2 border-primary-500 text-primary-600 dark:text-primary-400 hover:bg-primary-50 dark:hover:bg-primary-950/50 hover:border-primary-600 active:bg-primary-100 dark:active:bg-primary-950 shadow-md hover:shadow-lg hover:scale-105 active:scale-95 focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Download Data" > <span class="flex-shrink-0"> <svg class="w-4 h-4" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M19.5 14.25v-2.625a3.375 3.375 0 0 0-3.375-3.375h-1.5A1.125 1.125 0 0 1 13.5 7.125v-1.5a3.375 3.375 0 0 0-3.375-3.375H8.25m.75 12l3 3m0 0l3-3m-3 3v-6m-1.5-9H5.625c-.621 0-1.125.504-1.125 1.125v17.25c0 .621.504 1.125 1.125 1.125h12.75c.621 0 1.125-.504 1.125-1.125V11.25a9 9 0 0 0-9-9"/></svg> </span> <span>Download Data</span> </a> </div> <p> </p> <div class="text-left"> <a id="button-82291e5828e2086f9746d7778b8639e0" href="https://github.com/HugoBlox" target="_blank" rel="noopener noreferrer" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-transparent text-primary-600 dark:text-primary-400 hover:bg-primary-50 dark:hover:bg-primary-950/50 active:bg-primary-100 dark:active:bg-primary-950 hover:scale-105 active:scale-95 focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="View Source Code" > <span>View Source Code</span> <span class="flex-shrink-0"> <svg class="w-4 h-4" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.5 6H5.25A2.25 2.25 0 0 0 3 8.25v10.5A2.25 2.25 0 0 0 5.25 21h10.5A2.25 2.25 0 0 0 18 18.75V10.5m-10.5 6L21 3m0 0h-5.25M21 3v5.25"/></svg> </span> </a> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">style</span><span class="o">=</span><span class="s">"primary"</span><span class="w"> </span><span class="nx">size</span><span class="o">=</span><span class="s">"lg"</span><span class="w"> </span><span class="nx">align</span><span class="o">=</span><span class="s">"center"</span><span class="w"> </span><span class="nx">icon</span><span class="o">=</span><span class="s">"chart-bar"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>View Dashboard<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"/data/results.csv"</span><span class="w"> </span><span class="nx">style</span><span class="o">=</span><span class="s">"outline"</span><span class="w"> </span><span class="nx">icon</span><span class="o">=</span><span class="s">"document-arrow-down"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Download Data<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"https://github.com/HugoBlox"</span><span class="w"> </span><span class="nx">new_tab</span><span class="o">=</span><span class="s">"true"</span><span class="w"> </span><span class="nx">style</span><span class="o">=</span><span class="s">"ghost"</span><span class="w"> </span><span class="nx">icon</span><span class="o">=</span><span class="s">"arrow-top-right-on-square"</span><span class="w"> </span><span class="nx">icon_position</span><span class="o">=</span><span class="s">"right"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>View Source Code<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h3 id="multiple-aligned-buttons">Multiple Aligned Buttons</h3> <div class="text-center"> <a id="button-987a45b347d64631afb5ac08e8ba562e" href="https://jupyter.org/" target="_blank" rel="noopener noreferrer" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-secondary-500 to-secondary-600 hover:from-secondary-600 hover:to-secondary-700 active:from-secondary-700 active:to-secondary-800 text-white shadow-lg shadow-secondary-500/25 hover:shadow-xl hover:shadow-secondary-500/30 hover:scale-105 active:scale-95 focus:ring-secondary-500/50 px-4 py-2 text-base rounded-full" role="button" aria-label="Try Jupyter" > <span>Try Jupyter</span> </a> </div> <p> </p> <div class="text-center"> <a id="button-99f34fa8ea3f584e4353a18f5b12ea79" href="https://colab.research.google.com/" target="_blank" rel="noopener noreferrer" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-4 py-2 text-base rounded-full" role="button" aria-label="Open in Colab" > <span class="flex-shrink-0"> <svg class="w-4 h-4" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M15.59 14.37q.159.666.16 1.38a6 6 0 0 1-6 6v-4.8m5.84-2.58a14.98 14.98 0 0 0 6.16-12.12A14.98 14.98 0 0 0 9.631 8.41m5.96 5.96a14.9 14.9 0 0 1-5.841 2.58m-.119-8.54a6 6 0 0 0-7.381 5.84h4.8m2.581-5.84a14.9 14.9 0 0 0-2.58 5.84m2.699 2.7q-.155.032-.311.06a15 15 0 0 1-2.448-2.448l.06-.312m-2.24 2.39a4.49 4.49 0 0 0-1.757 4.306q.341.054.696.054a4.5 4.5 0 0 0 3.61-1.812M16.5 9a1.5 1.5 0 1 1-3 0a1.5 1.5 0 0 1 3 0"/></svg> </span> <span>Open in Colab</span> </a> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"https://jupyter.org/"</span><span class="w"> </span><span class="nx">new_tab</span><span class="o">=</span><span class="s">"true"</span><span class="w"> </span><span class="nx">style</span><span class="o">=</span><span class="s">"secondary"</span><span class="w"> </span><span class="nx">rounded</span><span class="o">=</span><span class="s">"full"</span><span class="w"> </span><span class="nx">align</span><span class="o">=</span><span class="s">"center"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Try Jupyter<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"https://colab.research.google.com/"</span><span class="w"> </span><span class="nx">new_tab</span><span class="o">=</span><span class="s">"true"</span><span class="w"> </span><span class="nx">style</span><span class="o">=</span><span class="s">"primary"</span><span class="w"> </span><span class="nx">rounded</span><span class="o">=</span><span class="s">"full"</span><span class="w"> </span><span class="nx">align</span><span class="o">=</span><span class="s">"center"</span><span class="w"> </span><span class="nx">icon</span><span class="o">=</span><span class="s">"rocket-launch"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Open in Colab<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h2 id="did-you-find-this-page-helpful-consider-sharing-it-">Did you find this page helpful? Consider sharing it 🙌</h2> </article> <article> <h1>AtlasLens: Metadata-centric exploration and analysis of single-cell atlases</h1> <p>Wed, 01 Jul 2026 00:00:00 +0000</p> </article> <article> <h1>Comparing machine learning methods predicting transcriptome from epigenome with applications to association studies</h1> <p>Wed, 01 Jul 2026 00:00:00 +0000</p> </article> <article> <h1>Enabling allele-specific analysis of epigenome data</h1> <p>Fri, 19 Jun 2026 00:00:00 +0000</p> <h2 id="project-description">Project Description</h2> <p>Linking enhancers to genes is difficult. The state-of-the-art appraoch to link regulatory regions to genes is using the generalized Activity-by-Contact approach (gABC) see . The thesis is about enhancing the exisiting workflow to handle allele-specific epigenome data.</p> <h2 id="research-goals">Research Goals</h2> <ul> <li>Adjust the to accommodate allele-specific epigenome signals</li> <li>Test the new pipeline on novel heart related epigenome data</li> </ul> <h2 id="prerequisites">Prerequisites</h2> <ul> <li>Python programming</li> <li>ideally some knowledge about epigenomics</li> </ul> <h2 id="how-to-apply">How to Apply</h2> <p>Send a short Email with a short motivation to the corresponding supervisor .</p> </article> <article> <h1>Expanding a Nextflow pipeline for histone-association studies</h1> <p>Fri, 19 Jun 2026 00:00:00 +0000</p> <h2 id="project-description">Project Description</h2> <p>The epigenome is the layer on top of the genome that regulates how genes are expressed. We developed a Nextflow pipeline that uses machine learning models, that were trained to predict gene expression from epigenome data, to find genes which are associated with specific conditions such as cancer.</p> <h2 id="research-goals">Research Goals</h2> <ul> <li>Adjust and expand the to find which regions differ between groups of samples.</li> <li>Add a test to find which transcription factors are enriched in those regions.</li> <li>Test the pipeline on heart related epigenome data.</li> </ul> <h2 id="prerequisites">Prerequisites</h2> <ul> <li>Python programming</li> <li>Ideally some knowledge about epigenomics</li> <li>Experience with Nextflow would help but not necessary</li> </ul> <h2 id="how-to-apply">How to Apply</h2> <p>Send a short Email with a short motivation to the corresponding supervisor .</p> </article> <article> <h1>Expanding a Nextflow pipeline for single-cell data</h1> <p>Fri, 19 Jun 2026 00:00:00 +0000</p> <h2 id="project-description">Project Description</h2> <p>The epigenome is the layer on top of the genome that regulates how genes are expressed. We developed a Nextflow pipeline that uses machine learning models, that were trained to predict gene expression from epigenome data, to find genes which are associated with specific conditions such as cancer. The current implementation works entirely on bulk data.</p> <h2 id="research-goals">Research Goals</h2> <ul> <li>Adjust and expand the to also allow the usage of single-cell data.</li> <li>Add input processing of single-cell data, which can then be given to pre-trained single-cell models.</li> <li>Test the pipeline on additional data.</li> </ul> <h2 id="prerequisites">Prerequisites</h2> <ul> <li>Python/R programming</li> <li>Ideally some knowledge about epigenomics</li> <li>Experience with Nextflow would help but not necessary</li> </ul> <h2 id="how-to-apply">How to Apply</h2> <p>Send a short Email with a short motivation to the corresponding supervisor .</p> </article> <article> <h1>Exploring the regulatory impact of non-coding genetic variants</h1> <p>Fri, 19 Jun 2026 00:00:00 +0000</p> <h2 id="overview">Overview</h2> <p>SNEEP is a computational method to identify regulatory Single Nucleotide Variants (rSNVs) that alter the binding sites of Transcription Factors (TFs). It can efficiently analyze large collections of genetic variants, such as GWAS datasets. SNEEP combines its statistical approach with cell type-specific regulatory to prioritize functional non-coding variants and connect them to their target genes.</p> <h2 id="applications">Applications</h2> <p>In a large-scale study of coronary artery disease, SNEEP was used to connect disease-associated variants to candidate target genes based on enhancer-gene interaction prediceted with the gABC-score across 45 cell types. In another cardiovascular disease studies, SNEEP identified thousands of regulatory SNPs and uncovered novel candidate disease genes, including non-coding RNAs with experimentally validated functions in cardiac disease models.</p> <h2 id="associated-publications">Associated Publications</h2> <div class="cite-list"> <h2>Linked publications</h2> <div class="pub-list-item view-citation" style="margin-bottom: 1rem"> <i class="far fa-file-alt pub-icon" aria-hidden="true"></i> <span class="article-metadata li-cite-author"> <span ><a href="">Dennis Hecker</a></span>, <span ><a href="">Xiaoning Song</a></span>, <span ><a href="">Nina Baumgarten</a></span>, <span ><a href="">Anastasiia Diagel</a></span>, <span ><a href="">Nikoletta Katsaouni</a></span>, <span ><a href="">Ling Li</a></span>, <span ><a href="">Shuangyue Li</a></span>, <span ><a href="">Ranjan Kumar Maji</a></span>, <span ><a href="">Fatemeh Behjati Ardakani</a></span>, <span ><a href="">Lijiang Ma</a></span>, <span ><a href="">Zhaolong Li</a></span>, <span ><a href="">Aldo Moggio</a></span>, <span ><a href="">Daniel Tews</a></span>, <span ><a href="">Hendrik Sager</a></span>, <span ><a href="">Lars Maegdefessel</a></span>, <span ><a href="">Martin Wabitsch</a></span>, <span >Johan L. M. Björkegren</span>, <span ><a href="">Heribert Schunkert</a></span>, <span ><a href="">Zhifen Chen</a></span>, <span ><a href="">Marcel H. Schulz</a></span> </span> (2026). <a href="https://cgm.uni-frankfurt.de/publications/hecker-cell-2026/" class="underline">Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci</a>. <em>Nature Communications</em>. <div class="flex flex-wrap space-x-3"> <button class="hb-attachment-link hb-attachment-link-small js-cite-clipboard cursor-pointer" type="button" data-filename="/publications/hecker-cell-2026/cite.bib"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M15.75 17.25v3.375c0 .621-.504 1.125-1.125 1.125h-9.75a1.125 1.125 0 0 1-1.125-1.125V7.875c0-.621.504-1.125 1.125-1.125H6.75a9 9 0 0 1 1.5.124m7.5 10.376h3.375c.621 0 1.125-.504 1.125-1.125V11.25c0-4.46-3.243-8.161-7.5-8.876a9 9 0 0 0-1.5-.124H9.375c-.621 0-1.125.504-1.125 1.125v3.5m7.5 10.375H9.375a1.125 1.125 0 0 1-1.125-1.125v-9.25m12 6.625v-1.875a3.375 3.375 0 0 0-3.375-3.375h-1.5a1.125 1.125 0 0 1-1.125-1.125v-1.5a3.375 3.375 0 0 0-3.375-3.375H9.75"/></svg> <span>Cite</span> </button> <a class="hb-attachment-link hb-attachment-link-small" href="https://doi.org/10.1038/s41467-026-70216-6" target="_blank" rel="noopener"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.19 8.688a4.5 4.5 0 0 1 1.242 7.244l-4.5 4.5a4.5 4.5 0 0 1-6.364-6.364l1.757-1.757m13.35-.622l1.757-1.757a4.5 4.5 0 0 0-6.364-6.364l-4.5 4.5a4.5 4.5 0 0 0 1.242 7.244"/></svg> DOI </a> </div> </div> <div class="pub-list-item view-citation" style="margin-bottom: 1rem"> <i class="far fa-file-alt pub-icon" aria-hidden="true"></i> <span class="article-metadata li-cite-author"> <span ><a href="">Nina Baumgarten</a></span>, <span ><a href="">Laura Rumpf</a></span>, <span ><a href="">Thorsten Kessler</a></span>, <span ><a href="">Marcel H. Schulz</a></span> </span> (2024). <a href="https://cgm.uni-frankfurt.de/publications/baumgarten-statistical-2024/" class="underline">A statistical approach for identifying single nucleotide variants that affect transcription factor binding</a>. <em>iScience</em>. <div class="flex flex-wrap space-x-3"> <button class="hb-attachment-link hb-attachment-link-small js-cite-clipboard cursor-pointer" type="button" data-filename="/publications/baumgarten-statistical-2024/cite.bib"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M15.75 17.25v3.375c0 .621-.504 1.125-1.125 1.125h-9.75a1.125 1.125 0 0 1-1.125-1.125V7.875c0-.621.504-1.125 1.125-1.125H6.75a9 9 0 0 1 1.5.124m7.5 10.376h3.375c.621 0 1.125-.504 1.125-1.125V11.25c0-4.46-3.243-8.161-7.5-8.876a9 9 0 0 0-1.5-.124H9.375c-.621 0-1.125.504-1.125 1.125v3.5m7.5 10.375H9.375a1.125 1.125 0 0 1-1.125-1.125v-9.25m12 6.625v-1.875a3.375 3.375 0 0 0-3.375-3.375h-1.5a1.125 1.125 0 0 1-1.125-1.125v-1.5a3.375 3.375 0 0 0-3.375-3.375H9.75"/></svg> <span>Cite</span> </button> <a class="hb-attachment-link hb-attachment-link-small" href="https://doi.org/10.1016/j.isci.2024.109765" target="_blank" rel="noopener"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.19 8.688a4.5 4.5 0 0 1 1.242 7.244l-4.5 4.5a4.5 4.5 0 0 1-6.364-6.364l1.757-1.757m13.35-.622l1.757-1.757a4.5 4.5 0 0 0-6.364-6.364l-4.5 4.5a4.5 4.5 0 0 0 1.242 7.244"/></svg> DOI </a> </div> </div> <div class="pub-list-item view-citation" style="margin-bottom: 1rem"> <i class="far fa-file-alt pub-icon" aria-hidden="true"></i> <span class="article-metadata li-cite-author"> <span ><a href="">Chaonan Zhu</a></span>, <span ><a href="">Nina Baumgarten</a></span>, <span ><a href="">Meiqian Wu</a></span>, <span ><a href="">Yue Wang</a></span>, <span ><a href="">Arka Provo Das</a></span>, <span ><a href="">Jaskiran Kaur</a></span>, <span ><a href="">Fatemeh Behjati Ardakani</a></span>, <span ><a href="">Thanh Thuy Duong</a></span>, <span ><a href="">Minh Duc Pham</a></span>, <span ><a href="">Maria Duda</a></span>, <span ><a href="">Stefanie Dimmeler</a></span>, <span ><a href="">Ting Yuan</a></span>, <span ><a href="">Marcel H. Schulz</a></span>, <span ><a href="">Jaya Krishnan</a></span> </span> (2023). <a href="https://cgm.uni-frankfurt.de/publications/zhu-cvd-associated-2023/" class="underline">CVD-associated SNPs with regulatory potential reveal novel non-coding disease genes</a>. <em>Human Genomics</em>. <div class="flex flex-wrap space-x-3"> <button class="hb-attachment-link hb-attachment-link-small js-cite-clipboard cursor-pointer" type="button" data-filename="/publications/zhu-cvd-associated-2023/cite.bib"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M15.75 17.25v3.375c0 .621-.504 1.125-1.125 1.125h-9.75a1.125 1.125 0 0 1-1.125-1.125V7.875c0-.621.504-1.125 1.125-1.125H6.75a9 9 0 0 1 1.5.124m7.5 10.376h3.375c.621 0 1.125-.504 1.125-1.125V11.25c0-4.46-3.243-8.161-7.5-8.876a9 9 0 0 0-1.5-.124H9.375c-.621 0-1.125.504-1.125 1.125v3.5m7.5 10.375H9.375a1.125 1.125 0 0 1-1.125-1.125v-9.25m12 6.625v-1.875a3.375 3.375 0 0 0-3.375-3.375h-1.5a1.125 1.125 0 0 1-1.125-1.125v-1.5a3.375 3.375 0 0 0-3.375-3.375H9.75"/></svg> <span>Cite</span> </button> <a class="hb-attachment-link hb-attachment-link-small" href="https://doi.org/10.1186/s40246-023-00513-4" target="_blank" rel="noopener"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.19 8.688a4.5 4.5 0 0 1 1.242 7.244l-4.5 4.5a4.5 4.5 0 0 1-6.364-6.364l1.757-1.757m13.35-.622l1.757-1.757a4.5 4.5 0 0 0-6.364-6.364l-4.5 4.5a4.5 4.5 0 0 0 1.242 7.244"/></svg> DOI </a> </div> </div> </div> </article> <article> <h1>Statistical analysis of liver disease transcriptomes</h1> <p>Fri, 19 Jun 2026 00:00:00 +0000</p> <h2 id="project-description">Project Description</h2> <p>Do you want to learn how large transcriptomics datasets from patients are being analyzed? This project is about the analysis of RNA-seq samples from patients with liver disease. The experimental design of the study is involved and therefore needs to be tailored to generate informative results. This project combines statistical analysis with an interesting biological question on a novel dataset from collaborators.</p> <h2 id="research-goals">Research Goals</h2> <ul> <li>Conduct meta-data aware analysis of liver-disease specific genes</li> <li>Compare with other patient cohort data to corroborate results</li> </ul> <h2 id="prerequisites">Prerequisites</h2> <ul> <li>Python experience</li> <li>Basic understanding of RNA-seq analyses</li> </ul> <h2 id="how-to-apply">How to Apply</h2> <p>Send a short Email with a short motivation to the corresponding supervisor .</p> </article> <article> <h1>Quality control for imaging-based spatial transcriptomics</h1> <p>Thu, 18 Jun 2026 00:00:00 +0000</p> <h2 id="quality-control-for-imaging-based-spatial-transcriptomics">Quality control for imaging-based spatial transcriptomics</h2> <p><strong>Imaging-based spatial transcriptomics</strong> platforms (e.g. <em>CosMx</em>, <em>MERSCOPE</em>, <em>Xenium</em>) resolve individual RNA molecules in intact tissue with sub-cellular resolution, but the resulting data carries <strong>technical</strong> and <strong>biological artefacts</strong> that are not always apparent from inspection:</p> <ol> <li>Transcript dropout on the cell level</li> <li>Under- or over-segmented cells</li> <li>Truncated cells at the edges of imaging tiles (FOVs)</li> <li>False-positive signal from control probes</li> </ol> <p>Left unaddressed, these artefacts silently interfere with every downstream analysis.</p> <h2 id="what-were-building-toward">What we’re building toward</h2> <p>We aim to build an <strong>R package</strong> for <strong>quality control (QC)</strong> of imaging-based spatial transcriptomics data. It operates directly on standard Seurat and SpatialExperiment objects, computing quality-control metrics at the cell and FOV level. Every check is implemented as a discrete, composable step: compute a metric, flag the cells it identifies, visualise the result, and optionally filter. This ensures that every decision remains visible and reversible. Two entry points are provided: an <strong>interactive R API</strong> for assembling custom pipelines from individual QC steps, and a <strong>command-line mode</strong> that runs a fixed pipeline and produces a self-contained QC report for reproducible, code-free runs.Its role is to surface quality problems clearly and consistently, leaving the final keep-or-discard call to the researcher.</p> <div class="cite-list"> </div> </article> <article> <h1>Christian Kolland</h1> <p>Wed, 17 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Carolin Becker</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Christina Wrobel (formerly Kalk)</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>David Rodriguez Morales</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Dennis Hecker</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Laura Rumpf</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Lea Sarial</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Marcel Weinberg</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Maxim Evsioukov</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Nikoletta Katsaouni</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Nina Baumgarten</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Paula Kilp</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Paulina Kunz</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Prof. Dr. Marcel Schulz</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Sasha Soustova</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Shamim Ashrafiyan</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Yaroslav Kosaretskii</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Zlatka Fischer</h1> <p>Tue, 02 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Improved RNA-DNA interaction calling suggests RNA-based gene regulation of phenotypic transitions</h1> <p>Mon, 01 Jun 2026 00:00:00 +0000</p> </article> <article> <h1>Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data</h1> <p>Fri, 01 May 2026 00:00:00 +0000</p> </article> <article> <h1>Prediction and evaluation of Split-ORFs using Ribo-seq data</h1> <p>Fri, 01 May 2026 00:00:00 +0000</p> </article> <article> <h1>Probing transcription factor subsets in gene regulatory networks</h1> <p>Fri, 01 May 2026 00:00:00 +0000</p> </article> <article> <h1>Quantifying Components in a Model Vaccine with Machine-Learning-Augmented Raman Spectroscopy</h1> <p>Fri, 01 May 2026 00:00:00 +0000</p> </article> <article> <h1>RANKOR: Direct Drug Prioritization from Bulk and Single-Cell Transcriptomic Signatures</h1> <p>Fri, 01 May 2026 00:00:00 +0000</p> </article> <article> <h1>Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci</h1> <p>Sun, 01 Mar 2026 00:00:00 +0000</p> </article> <article> <h1>Enhancing KLF15 activity in cardiomyocytes: a novel approach to prevent pathological reprogramming and fibrosis via nuclease-deficient dCas9VPR</h1> <p>Sun, 01 Mar 2026 00:00:00 +0000</p> </article> <article> <h1>Comparative cross-methodological analysis of the IDH-wildtype glioblastoma tumor microenvironment</h1> <p>Sun, 01 Feb 2026 00:00:00 +0000</p> </article> <article> <h1>Hierarchical Representation Learning for Drug Mechanism-of-Action Prediction from Gene Expression Data</h1> <p>Sun, 01 Feb 2026 00:00:00 +0000</p> </article> <article> <h1>miRXplain: explainable isomiR-aware microRNA target prediction using CLIP-L experiments and hybrid attention transformers</h1> <p>Sun, 01 Feb 2026 00:00:00 +0000</p> </article> <article> <h1>Cystine import and oxidative catabolism fuel vascular growth and repair via nutrient-responsive histone acetylation</h1> <p>Thu, 01 Jan 2026 00:00:00 +0000</p> </article> <article> <h1>Epigenetic control of metabolic identity across cell types</h1> <p>Mon, 01 Dec 2025 00:00:00 +0000</p> </article> <article> <h1>The transaminase-ω-amidase pathway senses oxidative stress to control glutamine metabolism and α-ketoglutarate levels in endothelial cells</h1> <p>Mon, 01 Dec 2025 00:00:00 +0000</p> </article> <article> <h1>TripLexicon: prediction and analysis of gene regulatory RNA-DNA interactions</h1> <p>Mon, 01 Dec 2025 00:00:00 +0000</p> </article> <article> <h1>Decoding heart failure subtypes with neural networks via differential explanation analysis</h1> <p>Sat, 01 Nov 2025 00:00:00 +0000</p> </article> <article> <h1>Vascular Niches Are the Primary Hotspots in Cardiac Aging</h1> <p>Sat, 01 Nov 2025 00:00:00 +0000</p> </article> <article> <h1>Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard</h1> <p>Wed, 01 Oct 2025 00:00:00 +0000</p> </article> <article> <h1>Revealing microRNA regulation in single cells</h1> <p>Sun, 01 Jun 2025 00:00:00 +0000</p> </article> <article> <h1>STAT3 expression is reduced in cardiac pericytes in HFpEF and its loss reduces cellular adhesion and induces pericyte senescence</h1> <p>Sun, 01 Jun 2025 00:00:00 +0000</p> </article> <article> <h1>A cell type-specific expression atlas of small and total RNA in the heart after myocardial infarction</h1> <p>Thu, 01 May 2025 00:00:00 +0000</p> </article> <article> <h1>GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data</h1> <p>Wed, 01 Jan 2025 00:00:00 +0000</p> </article> <article> <h1>Learning Enhancer-Gene associations from Bulk Transcriptomic and Epigenetic Sequencing Data with STITCHIT</h1> <p>Wed, 01 Jan 2025 00:00:00 +0000</p> </article> <article> <h1>Long non-coding RNAs direct the SWI/SNF complex to cell type-specific enhancers</h1> <p>Wed, 01 Jan 2025 00:00:00 +0000</p> </article> <article> <h1>Prediction of Enhancer-Gene Interactions Using Chromatin-Conformation Capture and Epigenome Data Using STARE</h1> <p>Wed, 01 Jan 2025 00:00:00 +0000</p> </article> <article> <h1>Temporal Expression Analysis to Unravel Gene Regulatory Dynamics by microRNAs</h1> <p>Wed, 01 Jan 2025 00:00:00 +0000</p> </article> <article> <h1>AtlasLens</h1> <p>Fri, 17 May 2024 00:00:00 +0000</p> <p>TODO: add description and logo</p> </article> <article> <h1>MetaFR</h1> <p>Fri, 17 May 2024 00:00:00 +0000</p> <p>TODO: add description and logo</p> </article> <article> <h1>RANKOR</h1> <p>Fri, 17 May 2024 00:00:00 +0000</p> <p>TODO: add description and logo</p> </article> <article> <h1>SNEEP</h1> <p>Fri, 17 May 2024 00:00:00 +0000</p> <p>SNEEP is a statistical approach to predict the effect of non-coding genetic variants on transcription factor (TF) binding sites. It scales to large genomic datasets and can integrate cell type specific genetic and epigenetic information such as open chromatin or expression data to prioritize functional non-coding variants. Further, by linking variants to target genes via enhancer-gene interactions, SNEEP enables mechanistic interpretation of genetic associations.</p> </article> <article> <h1>A statistical approach for identifying single nucleotide variants that affect transcription factor binding</h1> <p>Wed, 01 May 2024 00:00:00 +0000</p> </article> <article> <h1>BI-3231, an enzymatic inhibitor of HSD17B13, reduces lipotoxic effects induced by palmitic acid in murine and human hepatocytes</h1> <p>Fri, 01 Mar 2024 00:00:00 +0000</p> </article> <article> <h1>A systematic analysis of circRNAs in subnuclear compartments</h1> <p>Mon, 01 Jan 2024 00:00:00 +0000</p> </article> <article> <h1>An AI-based cell segmentation pipeline for studying immune markers from brightfield microscopy images</h1> <p>Mon, 01 Jan 2024 00:00:00 +0000</p> </article> <article> <h1>Improved integration of single-cell transcriptome data demonstrates common and unique signatures of heart failure in mice and humans</h1> <p>Mon, 01 Jan 2024 00:00:00 +0000</p> </article> <article> <h1>Multiomics analysis identifies novel facilitators of human dopaminergic neuron differentiation</h1> <p>Mon, 01 Jan 2024 00:00:00 +0000</p> </article> <article> <h1>Computational tools for inferring transcription factor activity</h1> <p>Fri, 01 Dec 2023 00:00:00 +0000</p> </article> <article> <h1>Categorization of Spatial Transcriptomics Methods for Cell-Cell Communication Analysis</h1> <p>Thu, 26 Oct 2023 00:00:00 +0000</p> <p>Cell–cell communication (CCC) plays a central role in regulating cellular behavior within tissues. Spatial transcriptomics provides the spatial context needed for biologically informed CCC analysis, leading to a rapidly growing landscape of computational methods. In this review, we evaluate 31 recent approaches, categorize them according to their analytical objectives, and provide practical guidance for selecting appropriate methods based on specific research questions.</p> <div class="cite-list"> </div> </article> <article> <h1>Enhancer-gene interactions and transcription factor affinities</h1> <p>Thu, 26 Oct 2023 00:00:00 +0000</p> <p>Enhancer–gene interactions are an important factor in epigenomics because they help to explain how regulatory regions control gene expression. Enhancers can act over large distances and do so in a cell type-specific manner. These interactions help connect epigenomic features to functional gene regulation, by finding regulatory programs that define cellular identity or provide interpretation for disease-associated noncoding variants.</p> <p>We developed STARE, a computational tool for assigning enhancers to their likely target genes and using those to summarize transcription factor affinity on gene-level. The enhancer-gene interactions are predicted with the generalized Activity-by-Contact (gABC)-score, which uses a measurement of enhancer activity and optionally also chromatin contact data. It can be applied to pseudobulked single-cell data as well.</p> <p>We applied STARE in a variety of different projects, especially the enhancer-gene interactions. Its applications so far include:</p> <ul> <li>Examining the role of an understudied histone modification during cardiogenesis</li> <li>Investigation of the relation between metabolism and epigenomics at the example of the cysteine pathway</li> <li>Prioritizing disease genes for coronary artery disease by interpreting the impact of genomic risk variants on gene regulation</li> <li>The role of <em>STAT3</em> in pericytes under HFpEF</li> </ul> </article> <article> <h1>MISPIL and/or PCMultiome</h1> <p>Thu, 26 Oct 2023 00:00:00 +0000</p> <p>We use gene-specific models to predict expression from epigenetic activity and perturb candidate regulatory elements in silico to identify small combinations that shift disease-associated expression profiles toward healthy states. By formulating this as a combinatorial optimization problem, we can efficiently prioritize regulatory regions for follow-up experimental perturbation.</p> <div class="cite-list"> </div> </article> <article> <h1>Prediction and evaluation of Split open reading frames</h1> <p>Thu, 26 Oct 2023 00:00:00 +0000</p> <p>The regulation of RNA translation is crucial for maintaining appropriate protein levels within cells. A novel mechanism which controls RNA translation is via the formation of Split open reading frames (Split-ORFs). These occur in transcripts containing at least two open reading frames, each encoding a part of the same full-length protein. These multiple open reading frames arise from alternatively spliced transcript isoforms. We developed the Split-ORF pipeline, a computational tool that predicts Split-ORFs from transcripts’ sequences and identifies regions unique to the predicted Split-ORF products for evaluation with Ribo-seq data.</p> </article> <article> <h1>Prediction of gene expression from epigenome data</h1> <p>Thu, 26 Oct 2023 00:00:00 +0000</p> <p>Prediction of gene expression from epigenome data is an important task to link epigenome variation to changes in gene expression. Over the years we have designed a number of machine learning methods that present approaches for learning those links. We have made a number of models available for the community in the EpiExpress repository that allows to conduct histone-acetylation based epigenome association studies.</p> <div class="cite-list"> <h2>Linked publications</h2> <div class="pub-list-item view-citation" style="margin-bottom: 1rem"> <i class="far fa-file-alt pub-icon" aria-hidden="true"></i> <span class="article-metadata li-cite-author"> <span ><a href="">Fatemeh Behjati Ardakani</a></span>, <span ><a href="">Shamim Ashrafiyan</a></span>, <span ><a href="">Laura Rumpf</a></span>, <span ><a href="">Dennis Hecker</a></span>, <span ><a href="">Marcel H Schulz</a></span> </span> (2026). <a href="https://cgm.uni-frankfurt.de/publications/behjati-ardakani-comparing-2026/" class="underline">Comparing machine learning methods predicting transcriptome from epigenome with applications to association studies</a>. <em>Genome Biology</em>. <div class="flex flex-wrap space-x-3"> <a class="hb-attachment-link hb-attachment-link-small" href="https://pubmed.ncbi.nlm.nih.gov/42444001/" target="_blank" rel="noopener"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.19 8.688a4.5 4.5 0 0 1 1.242 7.244l-4.5 4.5a4.5 4.5 0 0 1-6.364-6.364l1.757-1.757m13.35-.622l1.757-1.757a4.5 4.5 0 0 0-6.364-6.364l-4.5 4.5a4.5 4.5 0 0 0 1.242 7.244"/></svg> URL </a> <button class="hb-attachment-link hb-attachment-link-small js-cite-clipboard cursor-pointer" type="button" data-filename="/publications/behjati-ardakani-comparing-2026/cite.bib"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M15.75 17.25v3.375c0 .621-.504 1.125-1.125 1.125h-9.75a1.125 1.125 0 0 1-1.125-1.125V7.875c0-.621.504-1.125 1.125-1.125H6.75a9 9 0 0 1 1.5.124m7.5 10.376h3.375c.621 0 1.125-.504 1.125-1.125V11.25c0-4.46-3.243-8.161-7.5-8.876a9 9 0 0 0-1.5-.124H9.375c-.621 0-1.125.504-1.125 1.125v3.5m7.5 10.375H9.375a1.125 1.125 0 0 1-1.125-1.125v-9.25m12 6.625v-1.875a3.375 3.375 0 0 0-3.375-3.375h-1.5a1.125 1.125 0 0 1-1.125-1.125v-1.5a3.375 3.375 0 0 0-3.375-3.375H9.75"/></svg> <span>Cite</span> </button> <a class="hb-attachment-link hb-attachment-link-small" href="https://doi.org/10.1186/s13059-026-04131-w" target="_blank" rel="noopener"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.19 8.688a4.5 4.5 0 0 1 1.242 7.244l-4.5 4.5a4.5 4.5 0 0 1-6.364-6.364l1.757-1.757m13.35-.622l1.757-1.757a4.5 4.5 0 0 0-6.364-6.364l-4.5 4.5a4.5 4.5 0 0 0 1.242 7.244"/></svg> DOI </a> </div> </div> <div class="pub-list-item view-citation" style="margin-bottom: 1rem"> <i class="far fa-file-alt pub-icon" aria-hidden="true"></i> <span class="article-metadata li-cite-author"> <span ><a href="">Florian Schmidt</a></span>, <span ><a href="">Alexander Marx</a></span>, <span ><a href="">Nina Baumgarten</a></span>, <span ><a href="">Marie Hebel</a></span>, <span ><a href="">Martin Wegner</a></span>, <span ><a href="">Manuel Kaulich</a></span>, <span ><a href="">Matthias S. Leisegang</a></span>, <span ><a href="">Ralf P. Brandes</a></span>, <span >Jonathan Göke</span>, <span ><a href="">Jilles Vreeken</a></span>, <span ><a href="">Marcel H. Schulz</a></span> </span> (2021). <a href="https://cgm.uni-frankfurt.de/publications/schmidt-integrative-2021/" class="underline">Integrative analysis of epigenetics data identifies gene-specific regulatory elements</a>. <em>Nucleic Acids Research</em>. <div class="flex flex-wrap space-x-3"> <button class="hb-attachment-link hb-attachment-link-small js-cite-clipboard cursor-pointer" type="button" data-filename="/publications/schmidt-integrative-2021/cite.bib"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M15.75 17.25v3.375c0 .621-.504 1.125-1.125 1.125h-9.75a1.125 1.125 0 0 1-1.125-1.125V7.875c0-.621.504-1.125 1.125-1.125H6.75a9 9 0 0 1 1.5.124m7.5 10.376h3.375c.621 0 1.125-.504 1.125-1.125V11.25c0-4.46-3.243-8.161-7.5-8.876a9 9 0 0 0-1.5-.124H9.375c-.621 0-1.125.504-1.125 1.125v3.5m7.5 10.375H9.375a1.125 1.125 0 0 1-1.125-1.125v-9.25m12 6.625v-1.875a3.375 3.375 0 0 0-3.375-3.375h-1.5a1.125 1.125 0 0 1-1.125-1.125v-1.5a3.375 3.375 0 0 0-3.375-3.375H9.75"/></svg> <span>Cite</span> </button> <a class="hb-attachment-link hb-attachment-link-small" href="https://doi.org/10.1093/nar/gkab798" target="_blank" rel="noopener"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.19 8.688a4.5 4.5 0 0 1 1.242 7.244l-4.5 4.5a4.5 4.5 0 0 1-6.364-6.364l1.757-1.757m13.35-.622l1.757-1.757a4.5 4.5 0 0 0-6.364-6.364l-4.5 4.5a4.5 4.5 0 0 0 1.242 7.244"/></svg> DOI </a> </div> </div> <div class="pub-list-item view-citation" style="margin-bottom: 1rem"> <i class="far fa-file-alt pub-icon" aria-hidden="true"></i> <span class="article-metadata li-cite-author"> <span ><a href="">Florian Schmidt</a></span>, <span ><a href="">Fabian Kern</a></span>, <span ><a href="">Marcel H. Schulz</a></span> </span> (2020). <a href="https://cgm.uni-frankfurt.de/publications/schmidt-integrative-2020/" class="underline">Integrative prediction of gene expression with chromatin accessibility and conformation data</a>. <em>Epigenetics & Chromatin</em>. <div class="flex flex-wrap space-x-3"> <button class="hb-attachment-link hb-attachment-link-small js-cite-clipboard cursor-pointer" type="button" data-filename="/publications/schmidt-integrative-2020/cite.bib"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M15.75 17.25v3.375c0 .621-.504 1.125-1.125 1.125h-9.75a1.125 1.125 0 0 1-1.125-1.125V7.875c0-.621.504-1.125 1.125-1.125H6.75a9 9 0 0 1 1.5.124m7.5 10.376h3.375c.621 0 1.125-.504 1.125-1.125V11.25c0-4.46-3.243-8.161-7.5-8.876a9 9 0 0 0-1.5-.124H9.375c-.621 0-1.125.504-1.125 1.125v3.5m7.5 10.375H9.375a1.125 1.125 0 0 1-1.125-1.125v-9.25m12 6.625v-1.875a3.375 3.375 0 0 0-3.375-3.375h-1.5a1.125 1.125 0 0 1-1.125-1.125v-1.5a3.375 3.375 0 0 0-3.375-3.375H9.75"/></svg> <span>Cite</span> </button> <a class="hb-attachment-link hb-attachment-link-small" href="https://doi.org/10.1186/s13072-020-0327-0" target="_blank" rel="noopener"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.19 8.688a4.5 4.5 0 0 1 1.242 7.244l-4.5 4.5a4.5 4.5 0 0 1-6.364-6.364l1.757-1.757m13.35-.622l1.757-1.757a4.5 4.5 0 0 0-6.364-6.364l-4.5 4.5a4.5 4.5 0 0 0 1.242 7.244"/></svg> DOI </a> </div> </div> </div> </article> <article> <h1>Seda Nurhayat Öztürk</h1> <p>Thu, 26 Oct 2023 00:00:00 +0000</p> </article> <article> <h1>Signature reversal based drug ranking from expression data</h1> <p>Thu, 26 Oct 2023 00:00:00 +0000</p> <div class="cite-list"> <h2>Linked publications</h2> <div class="pub-list-item view-citation" style="margin-bottom: 1rem"> <i class="far fa-file-alt pub-icon" aria-hidden="true"></i> <span class="article-metadata li-cite-author"> <span ><a href="">Nikoletta Katsaouni</a></span>, <span ><a href="">Marcel H. Schulz</a></span> </span> (2026). <a href="https://cgm.uni-frankfurt.de/publications/katsaouni-rankor-2026/" class="underline">RANKOR: Direct Drug Prioritization from Bulk and Single-Cell Transcriptomic Signatures</a>. <em>Preprint (BioRxiv)</em>. <div class="flex flex-wrap space-x-3"> <a class="hb-attachment-link hb-attachment-link-small" href="http://biorxiv.org/lookup/doi/10.64898/2026.05.20.726471" target="_blank" rel="noopener"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.19 8.688a4.5 4.5 0 0 1 1.242 7.244l-4.5 4.5a4.5 4.5 0 0 1-6.364-6.364l1.757-1.757m13.35-.622l1.757-1.757a4.5 4.5 0 0 0-6.364-6.364l-4.5 4.5a4.5 4.5 0 0 0 1.242 7.244"/></svg> URL </a> <button class="hb-attachment-link hb-attachment-link-small js-cite-clipboard cursor-pointer" type="button" data-filename="/publications/katsaouni-rankor-2026/cite.bib"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M15.75 17.25v3.375c0 .621-.504 1.125-1.125 1.125h-9.75a1.125 1.125 0 0 1-1.125-1.125V7.875c0-.621.504-1.125 1.125-1.125H6.75a9 9 0 0 1 1.5.124m7.5 10.376h3.375c.621 0 1.125-.504 1.125-1.125V11.25c0-4.46-3.243-8.161-7.5-8.876a9 9 0 0 0-1.5-.124H9.375c-.621 0-1.125.504-1.125 1.125v3.5m7.5 10.375H9.375a1.125 1.125 0 0 1-1.125-1.125v-9.25m12 6.625v-1.875a3.375 3.375 0 0 0-3.375-3.375h-1.5a1.125 1.125 0 0 1-1.125-1.125v-1.5a3.375 3.375 0 0 0-3.375-3.375H9.75"/></svg> <span>Cite</span> </button> <a class="hb-attachment-link hb-attachment-link-small" href="https://doi.org/10.64898/2026.05.20.726471" target="_blank" rel="noopener"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.19 8.688a4.5 4.5 0 0 1 1.242 7.244l-4.5 4.5a4.5 4.5 0 0 1-6.364-6.364l1.757-1.757m13.35-.622l1.757-1.757a4.5 4.5 0 0 0-6.364-6.364l-4.5 4.5a4.5 4.5 0 0 0 1.242 7.244"/></svg> DOI </a> </div> </div> <div class="pub-list-item view-citation" style="margin-bottom: 1rem"> <i class="far fa-file-alt pub-icon" aria-hidden="true"></i> <span class="article-metadata li-cite-author"> <span ><a href="">Nikoletta Katsaouni</a></span>, <span ><a href="">Marcel H. Schulz</a></span> </span> (2026). <a href="https://cgm.uni-frankfurt.de/publications/katsaouni-hierarchical-2026/" class="underline">Hierarchical Representation Learning for Drug Mechanism-of-Action Prediction from Gene Expression Data</a>. <em>Preprint (BioRxiv)</em>. <div class="flex flex-wrap space-x-3"> <a class="hb-attachment-link hb-attachment-link-small" href="http://biorxiv.org/lookup/doi/10.64898/2026.02.03.703502" target="_blank" rel="noopener"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.19 8.688a4.5 4.5 0 0 1 1.242 7.244l-4.5 4.5a4.5 4.5 0 0 1-6.364-6.364l1.757-1.757m13.35-.622l1.757-1.757a4.5 4.5 0 0 0-6.364-6.364l-4.5 4.5a4.5 4.5 0 0 0 1.242 7.244"/></svg> URL </a> <button class="hb-attachment-link hb-attachment-link-small js-cite-clipboard cursor-pointer" type="button" data-filename="/publications/katsaouni-hierarchical-2026/cite.bib"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M15.75 17.25v3.375c0 .621-.504 1.125-1.125 1.125h-9.75a1.125 1.125 0 0 1-1.125-1.125V7.875c0-.621.504-1.125 1.125-1.125H6.75a9 9 0 0 1 1.5.124m7.5 10.376h3.375c.621 0 1.125-.504 1.125-1.125V11.25c0-4.46-3.243-8.161-7.5-8.876a9 9 0 0 0-1.5-.124H9.375c-.621 0-1.125.504-1.125 1.125v3.5m7.5 10.375H9.375a1.125 1.125 0 0 1-1.125-1.125v-9.25m12 6.625v-1.875a3.375 3.375 0 0 0-3.375-3.375h-1.5a1.125 1.125 0 0 1-1.125-1.125v-1.5a3.375 3.375 0 0 0-3.375-3.375H9.75"/></svg> <span>Cite</span> </button> <a class="hb-attachment-link hb-attachment-link-small" href="https://doi.org/10.64898/2026.02.03.703502" target="_blank" rel="noopener"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.19 8.688a4.5 4.5 0 0 1 1.242 7.244l-4.5 4.5a4.5 4.5 0 0 1-6.364-6.364l1.757-1.757m13.35-.622l1.757-1.757a4.5 4.5 0 0 0-6.364-6.364l-4.5 4.5a4.5 4.5 0 0 0 1.242 7.244"/></svg> DOI </a> </div> </div> </div> </article> <article> <h1>Embed Media</h1> <p>Tue, 24 Oct 2023 00:00:00 +0000</p> <p> is designed to give technical content creators a seamless experience. You can focus on the content and the HugoBlox Kit which this template is built upon handles the rest.</p> <p><strong>Embed videos, podcasts, code, LaTeX math, and even test students!</strong></p> <p>On this page, you’ll find some examples of the types of technical content that can be rendered with Hugo Blox.</p> <h2 id="video">Video</h2> <p>Teach your course by sharing videos with your students. Choose from one of the following approaches:</p> <div style="position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden;"> </div> <p><strong>Youtube</strong>:</p> <pre><code>{{< youtube w7Ft2ymGmfc >}} </code></pre> <p><strong>Bilibili</strong>:</p> <pre><code>{{< bilibili id="BV1WV4y1r7DF" >}} </code></pre> <p><strong>Video file</strong></p> <p>Videos may be added to a page by either placing them in your <code>assets/media/</code> media library or in your , and then embedding them with the <em>video</em> shortcode:</p> <pre><code>{{< video src="my_video.mp4" controls="yes" >}} </code></pre> <h2 id="podcast">Podcast</h2> <p>You can add a podcast or music to a page by placing the MP3 file in the page’s folder or the media library folder and then embedding the audio on your page with the <em>audio</em> shortcode:</p> <pre><code>{{< audio src="ambient-piano.mp3" >}} </code></pre> <p>Try it out:</p> </audio> <h2 id="test-students">Test students</h2> <p>Provide a simple yet fun self-assessment by revealing the solutions to challenges with the <code>spoiler</code> shortcode:</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl">{{< spoiler text="👉 Click to view the solution" >}} </span></span><span class="line"><span class="cl">You found me! </span></span><span class="line"><span class="cl">{{< /spoiler >}} </span></span></code></pre></div><p>renders as</p> <details class="spoiler " id="spoiler-2"> <summary class="cursor-pointer">👉 Click to view the solution</summary> <div class="rounded-lg bg-neutral-50 dark:bg-neutral-800 p-2"> You found me 🎉 </div> </details> <h2 id="math">Math</h2> <p>HugoBlox Kit supports a Markdown extension for $\LaTeX$ math. You can enable this feature by toggling the <code>math</code> option in your <code>config/_default/params.yaml</code> file.</p> <p>To render <em>inline</em> or <em>block</em> math, wrap your LaTeX math with <code>{{< math >}}$...${{< /math >}}</code> or <code>{{< math >}}$$...$${{< /math >}}</code>, respectively.</p> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-blue-100 dark:bg-blue-900 border-blue-500" data-callout="note" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-blue-600 dark:text-blue-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="m16.862 4.487l1.687-1.688a1.875 1.875 0 1 1 2.652 2.652L6.832 19.82a4.5 4.5 0 0 1-1.897 1.13l-2.685.8l.8-2.685a4.5 4.5 0 0 1 1.13-1.897zm0 0L19.5 7.125"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Note</div> <div class="callout-body"><p>We wrap the LaTeX math in the Hugo Blox <em>math</em> shortcode to prevent Hugo rendering our math as Markdown. This callout now uses the standard Markdown alert syntax!</p></div> </div> </div> <p>Example <strong>math block</strong>:</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-latex" data-lang="latex"><span class="line"><span class="cl"><span class="nb">{{</span>< math ><span class="nb">}}</span> </span></span><span class="line"><span class="cl"><span class="sb">$$</span><span class="nb"> </span></span></span><span class="line"><span class="cl"><span class="nv">\gamma</span><span class="nb">_{n} </span><span class="o">=</span><span class="nb"> </span><span class="nv">\frac</span><span class="nb">{ </span><span class="nv">\left</span><span class="nb"> | </span><span class="nv">\left</span><span class="nb"> </span><span class="o">(</span><span class="nv">\mathbf</span><span class="nb"> x_{n} </span><span class="o">-</span><span class="nb"> </span><span class="nv">\mathbf</span><span class="nb"> x_{n</span><span class="o">-</span><span class="m">1</span><span class="nb">} </span><span class="nv">\right</span><span class="nb"> </span><span class="o">)</span><span class="nb">^T </span><span class="nv">\left</span><span class="nb"> </span><span class="o">[</span><span class="nv">\nabla</span><span class="nb"> F </span><span class="o">(</span><span class="nv">\mathbf</span><span class="nb"> x_{n}</span><span class="o">)</span><span class="nb"> </span><span class="o">-</span><span class="nb"> </span><span class="nv">\nabla</span><span class="nb"> F </span><span class="o">(</span><span class="nv">\mathbf</span><span class="nb"> x_{n</span><span class="o">-</span><span class="m">1</span><span class="nb">}</span><span class="o">)</span><span class="nb"> </span><span class="nv">\right</span><span class="nb"> </span><span class="o">]</span><span class="nb"> </span><span class="nv">\right</span><span class="nb"> |}{</span><span class="nv">\left</span><span class="nb"> </span><span class="nv">\|\nabla</span><span class="nb"> F</span><span class="o">(</span><span class="nv">\mathbf</span><span class="nb">{x}_{n}</span><span class="o">)</span><span class="nb"> </span><span class="o">-</span><span class="nb"> </span><span class="nv">\nabla</span><span class="nb"> F</span><span class="o">(</span><span class="nv">\mathbf</span><span class="nb">{x}_{n</span><span class="o">-</span><span class="m">1</span><span class="nb">}</span><span class="o">)</span><span class="nb"> </span><span class="nv">\right</span><span class="nb"> </span><span class="nv">\|</span><span class="nb">^</span><span class="m">2</span><span class="nb">} </span></span></span><span class="line"><span class="cl"><span class="s">$$</span> </span></span><span class="line"><span class="cl"><span class="nb">{{</span>< /math ><span class="nb">}}</span> </span></span></code></pre></div><p>renders as</p> $$\gamma_{n} = \frac{ \left | \left (\mathbf x_{n} - \mathbf x_{n-1} \right )^T \left [\nabla F (\mathbf x_{n}) - \nabla F (\mathbf x_{n-1}) \right ] \right |}{\left \|\nabla F(\mathbf{x}_{n}) - \nabla F(\mathbf{x}_{n-1}) \right \|^2}$$ <p>Example <strong>inline math</strong> <code>{{< math >}}$\nabla F(\mathbf{x}_{n})${{< /math >}}</code> renders as $\nabla F(\mathbf{x}_{n})$ .</p> <p>Example <strong>multi-line math</strong> using the math linebreak (<code>\\</code>):</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-latex" data-lang="latex"><span class="line"><span class="cl"><span class="nb">{{</span>< math ><span class="nb">}}</span> </span></span><span class="line"><span class="cl"><span class="sb">$$</span><span class="nb">f</span><span class="o">(</span><span class="nb">k;p_{</span><span class="m">0</span><span class="nb">}^{</span><span class="o">*</span><span class="nb">}</span><span class="o">)</span><span class="nb"> </span><span class="o">=</span><span class="nb"> </span><span class="nv">\begin</span><span class="nb">{cases}p_{</span><span class="m">0</span><span class="nb">}^{</span><span class="o">*</span><span class="nb">} & </span><span class="nv">\text</span><span class="nb">{if }k</span><span class="o">=</span><span class="m">1</span><span class="nb">, </span><span class="nv">\\</span><span class="nb"> </span></span></span><span class="line"><span class="cl"><span class="m">1</span><span class="o">-</span><span class="nb">p_{</span><span class="m">0</span><span class="nb">}^{</span><span class="o">*</span><span class="nb">} & </span><span class="nv">\text</span><span class="nb">{if }k</span><span class="o">=</span><span class="m">0</span><span class="nb">.</span><span class="nv">\end</span><span class="nb">{cases}</span><span class="s">$$</span> </span></span><span class="line"><span class="cl"><span class="nb">{{</span>< /math ><span class="nb">}}</span> </span></span></code></pre></div><p>renders as</p> $$ f(k;p_{0}^{*}) = \begin{cases}p_{0}^{*} & \text{if }k=1, \\ 1-p_{0}^{*} & \text{if }k=0.\end{cases} $$ <h2 id="code">Code</h2> <p>HugoBlox Kit utilises Hugo’s Markdown extension for highlighting code syntax. The code theme can be selected in the <code>config/_default/params.yaml</code> file.</p> <pre><code>```python import pandas as pd data = pd.read_csv("data.csv") data.head() ``` </code></pre> <p>renders as</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-python" data-lang="python"><span class="line"><span class="cl"><span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span> </span></span><span class="line"><span class="cl"><span class="n">data</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="s2">"data.csv"</span><span class="p">)</span> </span></span><span class="line"><span class="cl"><span class="n">data</span><span class="o">.</span><span class="n">head</span><span class="p">()</span> </span></span></code></pre></div><h2 id="inline-images">Inline Images</h2> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go" data-lang="go"><span class="line"><span class="cl"><span class="p">{{<</span><span class="w"> </span><span class="nx">icon</span><span class="w"> </span><span class="nx">name</span><span class="p">=</span><span class="s">"python"</span><span class="w"> </span><span class="p">>}}</span><span class="w"> </span><span class="nx">Python</span><span class="w"> </span></span></span></code></pre></div><p>renders as</p> <p> <span class="inline-block pr-1"> <svg style="height: 1em; transform: translateY(0.1em);" xmlns="http://www.w3.org/2000/svg" height="1em" viewBox="0 0 448 512" fill="currentColor"><path d="M439.8 200.5c-7.7-30.9-22.3-54.2-53.4-54.2h-40.1v47.4c0 36.8-31.2 67.8-66.8 67.8H172.7c-29.2 0-53.4 25-53.4 54.3v101.8c0 29 25.2 46 53.4 54.3 33.8 9.9 66.3 11.7 106.8 0 26.9-7.8 53.4-23.5 53.4-54.3v-40.7H226.2v-13.6h160.2c31.1 0 42.6-21.7 53.4-54.2 11.2-33.5 10.7-65.7 0-108.6zM286.2 404c11.1 0 20.1 9.1 20.1 20.3 0 11.3-9 20.4-20.1 20.4-11 0-20.1-9.2-20.1-20.4.1-11.3 9.1-20.3 20.1-20.3zM167.8 248.1h106.8c29.7 0 53.4-24.5 53.4-54.3V91.9c0-29-24.4-50.7-53.4-55.6-35.8-5.9-74.7-5.6-106.8.1-45.2 8-53.4 24.7-53.4 55.6v40.7h106.9v13.6h-147c-31.1 0-58.3 18.7-66.8 54.2-9.8 40.7-10.2 66.1 0 108.6 7.6 31.6 25.7 54.2 56.8 54.2H101v-48.8c0-35.3 30.5-66.4 66.8-66.4zm-6.7-142.6c-11.1 0-20.1-9.1-20.1-20.3.1-11.3 9-20.4 20.1-20.4 11 0 20.1 9.2 20.1 20.4s-9 20.3-20.1 20.3z"/></svg> </span> Python</p> <h2 id="did-you-find-this-page-helpful-consider-sharing-it-">Did you find this page helpful? 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It can be combined with gene annotation to provide gene-level estimates of TF regulation.</p> </article> <article> <h1>Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development</h1> <p>Tue, 01 Nov 2016 00:00:00 +0000</p> </article> <article> <h1>The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery</h1> <p>Tue, 01 Nov 2016 00:00:00 +0000</p> </article> <article> <h1>Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgenes</h1> <p>Fri, 01 Jul 2016 00:00:00 +0000</p> </article> <article> <h1>Informed kmer selection for de novo transcriptome assembly</h1> <p>Wed, 01 Jun 2016 00:00:00 +0000</p> </article> <article> <h1>KREATION</h1> <p>Thu, 28 Apr 2016 00:00:00 +0000</p> <p>KREATION is meta-software that enables parameter selection for de novo transcriptome assemblers. It also has a missassembly filter that can be used to improve the quality of assemblies.</p> </article> <article> <h1>De novo ChIP-seq analysis</h1> <p>Tue, 01 Sep 2015 00:00:00 +0000</p> </article> <article> <h1>Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia</h1> <p>Sat, 01 Aug 2015 00:00:00 +0000</p> </article> <article> <h1>A general concept for consistent documentation of computational analyses</h1> <p>Thu, 01 Jan 2015 00:00:00 +0000</p> </article> <article> <h1>Fiona: a parallel and automatic strategy for read error correction</h1> <p>Mon, 01 Sep 2014 00:00:00 +0000</p> </article> <article> <h1>Fiona</h1> <p>Fri, 22 Aug 2014 00:00:00 +0000</p> <p>Fiona is a genome read error correction method that corrects indel and substitution errors using several word lengths. It automatically adapts the parameters to the data and supports OpenMP parallelization.</p> </article> <article> <h1>Letting the data speak for themselves: a fully Bayesian approach to transcriptome assembly</h1> <p>Wed, 01 Jan 2014 00:00:00 +0000</p> </article> <article> <h1>Assessment of transcript reconstruction methods for RNA-seq</h1> <p>Sun, 01 Dec 2013 00:00:00 +0000</p> </article> <article> <h1>Reconstructing dynamic microRNA-regulated interaction networks</h1> <p>Sun, 01 Sep 2013 00:00:00 +0000</p> </article> <article> <h1>Probabilistic error correction for RNA sequencing</h1> <p>Wed, 01 May 2013 00:00:00 +0000</p> </article> <article> <h1>SEECER</h1> <p>Wed, 03 Apr 2013 00:00:00 +0000</p> <p>SEquencing Error CorrEction for RNA sequencing data (SEECER) is a read error correction method designed for non-uniform sequencing data sets, in particular RNA-seq. It clusters reads and reconstructs profile HMMs to correct indel and substitution errors with high sensitivity.</p> </article> <article> <h1>Bayesian ontology querying for accurate and noise-tolerant semantic searches</h1> <p>Mon, 01 Oct 2012 00:00:00 +0000</p> </article> <article> <h1>DREM 2.0</h1> <p>Thu, 16 Aug 2012 00:00:00 +0000</p> <p>DREM is a input/output HMM based method to reconstruct dynamic maps of TF regulation using expression time series data. The software is written in Java and has a rich user interface for network display and downstream analyses.</p> </article> <article> <h1>DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data</h1> <p>Wed, 01 Aug 2012 00:00:00 +0000</p> </article> <article> <h1>Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels</h1> <p>Sun, 01 Apr 2012 00:00:00 +0000</p> </article> <article> <h1>Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS</h1> <p>Thu, 01 Mar 2012 00:00:00 +0000</p> </article> <article> <h1>Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts</h1> <p>Thu, 01 Mar 2012 00:00:00 +0000</p> </article> <article> <h1>Oases</h1> <p>Fri, 24 Feb 2012 00:00:00 +0000</p> <p>Oases is a de novo transcriptome assembler that exploits similarities between de Bruijn graphs and splicing graphs to reconstructs full length mRNAs from RNA-Seq data with high sensitivity and is one of the most widely used methods in its class.</p> </article> <article> <h1>ALF</h1> <p>Thu, 12 Jan 2012 00:00:00 +0000</p> <p>ALF is a toolbox of alignment-free sequence similarity measures, including a new measure, N2, that includes mismatches and the reverse complement of words. We have shown that N2 outperforms other common alignment-free measures in performance and runtime, it was desinged to accomodate inexact overlaps as in degenerate binding sites or reads with sequencing errors.</p> </article> <article> <h1>SplazerS</h1> <p>Wed, 11 Jan 2012 00:00:00 +0000</p> <p>SplazerS is a split-read indel alignment method with high sensitivity that works for single and paired-end reads.</p> </article> <article> <h1>A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins NonO and SFPQ</h1> <p>Thu, 01 Dec 2011 00:00:00 +0000</p> </article> <article> <h1>Exact score distribution computation for ontological similarity searches</h1> <p>Tue, 01 Nov 2011 00:00:00 +0000</p> </article> <article> <h1>DECOD: fast and accurate discriminative DNA motif finding</h1> <p>Thu, 01 Sep 2011 00:00:00 +0000</p> </article> <article> <h1>Integrative analysis of genomic, functional and protein interaction data predicts long-range enhancer-target gene interactions</h1> <p>Fri, 01 Apr 2011 00:00:00 +0000</p> </article> <article> <h1>Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments</h1> <p>Tue, 01 Jun 2010 00:00:00 +0000</p> </article> <article> <h1>Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads</h1> <p>Sun, 01 Nov 2009 00:00:00 +0000</p> </article> <article> <h1>Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts</h1> <p>Sun, 01 Nov 2009 00:00:00 +0000</p> </article> <article> <h1>Phenomizer</h1> <p>Fri, 09 Oct 2009 00:00:00 +0000</p> <p>The Phenomizer is an online webservice for clinical diagnosis. The physician can can query the database to get predictions of the best matching disease for a set of observed phenotypes.</p> </article> <article> <h1>Clinical diagnostics in human genetics with semantic similarity searches in ontologies</h1> <p>Thu, 01 Oct 2009 00:00:00 +0000</p> </article> <article> <h1>A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome</h1> <p>Fri, 01 Aug 2008 00:00:00 +0000</p> </article> <article> <h1>Mapping translocation breakpoints by next-generation sequencing</h1> <p>Tue, 01 Jul 2008 00:00:00 +0000</p> </article> <article> <h1>A short ultraconserved sequence drives transcription from an alternate FBN1 promoter</h1> <p>Tue, 01 Jan 2008 00:00:00 +0000</p> </article> <article> <h1>The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences</h1> <p>Tue, 01 Jan 2008 00:00:00 +0000</p> </article> <article> <h1>A unified single-cell atlas of mouse tissue damage</h1> <p>Mon, 01 Jan 0001 00:00:00 +0000</p> <p>Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into cellular responses across tissues and disease states. As part of the collaborative efforts of the SFB 1531 consortium, with contributions from multiple research groups, we constructed an integrated atlas of approximately 390,000 mouse cells spanning multiple tissues (heart, carotid, lung, and brain) and disease models, including heart disease, stroke, and lung injury. To harmonize technical and biological variation across datasets, we applied scVI to integrate raw count data while effectively removing batch effects. Cell types were annotated using curated marker genes from the literature. This comprehensive atlas serves as a unique resource for a wide range of downstream analyses, including the identification of disease-specific and shared transcriptional programs, differential gene expression analysis, gene–disease association studies, dynamic transcription factor network inference, and the integration of spatial transcriptomics data.</p> <div class="cite-list"> <h2>Linked publications</h2> <div class="pub-list-item view-citation" style="margin-bottom: 1rem"> <i class="far fa-file-alt pub-icon" aria-hidden="true"></i> <span class="article-metadata li-cite-author"> <span ><a href="">Shamim Ashrafiyan</a></span>, <span ><a href="">Iaroslav Kosaretskii</a></span>, <span ><a href="">Marcel H. Schulz</a></span> </span> (2026). <a href="https://cgm.uni-frankfurt.de/publications/ashrafiyan-atlaslens-2026/" class="underline">AtlasLens: Metadata-centric exploration and analysis of single-cell atlases</a>. <em>Preprint (BioRxiv)</em>. <div class="flex flex-wrap space-x-3"> <a class="hb-attachment-link hb-attachment-link-small" href="https://www.biorxiv.org/content/10.64898/2026.07.10.735823v1" target="_blank" rel="noopener"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.19 8.688a4.5 4.5 0 0 1 1.242 7.244l-4.5 4.5a4.5 4.5 0 0 1-6.364-6.364l1.757-1.757m13.35-.622l1.757-1.757a4.5 4.5 0 0 0-6.364-6.364l-4.5 4.5a4.5 4.5 0 0 0 1.242 7.244"/></svg> URL </a> <button class="hb-attachment-link hb-attachment-link-small js-cite-clipboard cursor-pointer" type="button" data-filename="/publications/ashrafiyan-atlaslens-2026/cite.bib"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M15.75 17.25v3.375c0 .621-.504 1.125-1.125 1.125h-9.75a1.125 1.125 0 0 1-1.125-1.125V7.875c0-.621.504-1.125 1.125-1.125H6.75a9 9 0 0 1 1.5.124m7.5 10.376h3.375c.621 0 1.125-.504 1.125-1.125V11.25c0-4.46-3.243-8.161-7.5-8.876a9 9 0 0 0-1.5-.124H9.375c-.621 0-1.125.504-1.125 1.125v3.5m7.5 10.375H9.375a1.125 1.125 0 0 1-1.125-1.125v-9.25m12 6.625v-1.875a3.375 3.375 0 0 0-3.375-3.375h-1.5a1.125 1.125 0 0 1-1.125-1.125v-1.5a3.375 3.375 0 0 0-3.375-3.375H9.75"/></svg> <span>Cite</span> </button> <a class="hb-attachment-link hb-attachment-link-small" href="https://doi.org/10.64898/2026.07.10.735823" target="_blank" rel="noopener"> <svg style="height: 1em" class='inline-block' xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.19 8.688a4.5 4.5 0 0 1 1.242 7.244l-4.5 4.5a4.5 4.5 0 0 1-6.364-6.364l1.757-1.757m13.35-.622l1.757-1.757a4.5 4.5 0 0 0-6.364-6.364l-4.5 4.5a4.5 4.5 0 0 0 1.242 7.244"/></svg> DOI </a> </div> </div> </div> </article> <article> <h1>Buttons</h1> <p>Mon, 01 Jan 0001 00:00:00 +0000</p> <p>A modern, customizable button shortcode with gradient styling, icons, and smart link handling.</p> <h2 id="basic-usage">Basic Usage</h2> <div class="text-left"> <a id="button-351ac412531c23e422b81c6422c17da5" href="https://cgm.uni-frankfurt.de/contact" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Contact Us" > <span>Contact Us</span> </a> </div> <div class="text-left"> <a id="button-99f90e9d2b754ffe3fc7b4f9d280ab9e" href="https://example.com" target="_blank" rel="noopener noreferrer" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-secondary-500 to-secondary-600 hover:from-secondary-600 hover:to-secondary-700 active:from-secondary-700 active:to-secondary-800 text-white shadow-lg shadow-secondary-500/25 hover:shadow-xl hover:shadow-secondary-500/30 hover:scale-105 active:scale-95 focus:ring-secondary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Visit External Site" > <span>Visit External Site</span> </a> </div> <p>The above buttons are created with:</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"/contact"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Contact Us<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"https://example.com"</span><span class="w"> </span><span class="nx">new_tab</span><span class="o">=</span><span class="s">"true"</span><span class="w"> </span><span class="nx">style</span><span class="o">=</span><span class="s">"secondary"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Visit External Site<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h2 id="style-variants">Style Variants</h2> <h3 id="primary-default">Primary (Default)</h3> <div class="text-left"> <a id="button-33f0c5949dceb4f2158940543a6d11f0" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Primary Button" > <span>Primary Button</span> </a> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">style</span><span class="o">=</span><span class="s">"primary"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Primary Button<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h3 id="secondary">Secondary</h3> <div class="text-left"> <a id="button-654c665d9c02125e00b3c2638e02ff31" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-secondary-500 to-secondary-600 hover:from-secondary-600 hover:to-secondary-700 active:from-secondary-700 active:to-secondary-800 text-white shadow-lg shadow-secondary-500/25 hover:shadow-xl hover:shadow-secondary-500/30 hover:scale-105 active:scale-95 focus:ring-secondary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Secondary Button" > <span>Secondary Button</span> </a> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">style</span><span class="o">=</span><span class="s">"secondary"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Secondary Button<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h3 id="outline">Outline</h3> <div class="text-left"> <a id="button-569954ebe8d760dfbd5f8dd8d491e972" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-white dark:bg-zinc-900 border-2 border-primary-500 text-primary-600 dark:text-primary-400 hover:bg-primary-50 dark:hover:bg-primary-950/50 hover:border-primary-600 active:bg-primary-100 dark:active:bg-primary-950 shadow-md hover:shadow-lg hover:scale-105 active:scale-95 focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Outline Button" > <span>Outline Button</span> </a> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">style</span><span class="o">=</span><span class="s">"outline"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Outline Button<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h3 id="ghost">Ghost</h3> <div class="text-left"> <a id="button-e8d694dcc82ccc6b692376347eb1210c" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-transparent text-primary-600 dark:text-primary-400 hover:bg-primary-50 dark:hover:bg-primary-950/50 active:bg-primary-100 dark:active:bg-primary-950 hover:scale-105 active:scale-95 focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Ghost Button" > <span>Ghost Button</span> </a> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">style</span><span class="o">=</span><span class="s">"ghost"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Ghost Button<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h2 id="sizes">Sizes</h2> <h3 id="small">Small</h3> <div class="text-left"> <a id="button-9edd9a4164984b892472dc4cb0d94acb" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-3 py-1.5 text-sm rounded-lg" role="button" aria-label="Small Button" > <span>Small Button</span> </a> </div> <h3 id="medium-default">Medium (Default)</h3> <div class="text-left"> <a id="button-917c91b5df194ee244bcb8dd7d4916c5" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Medium Button" > <span>Medium Button</span> </a> </div> <h3 id="large">Large</h3> <div class="text-left"> <a id="button-c9ef1eeebbeac0de80c5666baeda508c" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-6 py-3 text-lg rounded-lg" role="button" aria-label="Large Button" > <span>Large Button</span> </a> </div> <h3 id="extra-large">Extra Large</h3> <div class="text-left"> <a id="button-c38da6a61bc9a2511c12a071b05d1527" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-8 py-4 text-xl rounded-lg" role="button" aria-label="Extra Large" > <span>Extra Large</span> </a> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">size</span><span class="o">=</span><span class="s">"sm"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Small Button<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">size</span><span class="o">=</span><span class="s">"md"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Medium Button<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">size</span><span class="o">=</span><span class="s">"lg"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Large Button<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">size</span><span class="o">=</span><span class="s">"xl"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Extra Large<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h2 id="alignment">Alignment</h2> <h3 id="left-default">Left (Default)</h3> <div class="text-left"> <a id="button-46275a2130718485193b07442854e305" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Left Aligned" > <span>Left Aligned</span> </a> </div> <h3 id="center">Center</h3> <div class="text-center"> <a id="button-2e7c6d0545131be865f91f4dcb47ebd3" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Center Aligned" > <span>Center Aligned</span> </a> </div> <h3 id="right">Right</h3> <div class="text-right"> <a id="button-09d01d6786049ba2a63f2cafd484e60e" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Right Aligned" > <span>Right Aligned</span> </a> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">align</span><span class="o">=</span><span class="s">"left"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Left Aligned<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">align</span><span class="o">=</span><span class="s">"center"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Center Aligned<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">align</span><span class="o">=</span><span class="s">"right"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Right Aligned<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h2 id="with-icons">With Icons</h2> <h3 id="icon-before-text">Icon Before Text</h3> <div class="text-left"> <a id="button-2070b64a1b12b8165d04699a5e4f0a4d" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Download" > <span class="flex-shrink-0"> <svg class="w-4 h-4" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M3 16.5v2.25A2.25 2.25 0 0 0 5.25 21h13.5A2.25 2.25 0 0 0 21 18.75V16.5M16.5 12L12 16.5m0 0L7.5 12m4.5 4.5V3"/></svg> </span> <span>Download</span> </a> </div> <h3 id="icon-after-text">Icon After Text</h3> <div class="text-left"> <a id="button-213c46a162adc66071b38a55c26716e3" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Continue" > <span>Continue</span> <span class="flex-shrink-0"> <svg class="w-4 h-4" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.5 4.5L21 12m0 0l-7.5 7.5M21 12H3"/></svg> </span> </a> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">icon</span><span class="o">=</span><span class="s">"arrow-down-tray"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Download<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">icon</span><span class="o">=</span><span class="s">"arrow-right"</span><span class="w"> </span><span class="nx">icon_position</span><span class="o">=</span><span class="s">"right"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Continue<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h2 id="rounded-corners">Rounded Corners</h2> <h3 id="small-radius">Small Radius</h3> <div class="text-left"> <a id="button-f306324e9ea3297cc7149761131e0e41" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-4 py-2 text-base rounded" role="button" aria-label="Small Radius" > <span>Small Radius</span> </a> </div> <h3 id="medium-radius-default">Medium Radius (Default)</h3> <div class="text-left"> <a id="button-d519a3255417739cb8197b9869248dec" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="Medium Radius" > <span>Medium Radius</span> </a> </div> <h3 id="large-radius">Large Radius</h3> <div class="text-left"> <a id="button-920afdfab9e2ab0e88cb5046924cd223" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-4 py-2 text-base rounded-xl" role="button" aria-label="Large Radius" > <span>Large Radius</span> </a> </div> <h3 id="pill-shape">Pill Shape</h3> <div class="text-left"> <a id="button-464be1a963c8f63cf75275ea2137551a" href="#" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-4 py-2 text-base rounded-full" role="button" aria-label="Pill Button" > <span>Pill Button</span> </a> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">rounded</span><span class="o">=</span><span class="s">"sm"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Small Radius<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">rounded</span><span class="o">=</span><span class="s">"md"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Medium Radius<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">rounded</span><span class="o">=</span><span class="s">"lg"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Large Radius<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"#"</span><span class="w"> </span><span class="nx">rounded</span><span class="o">=</span><span class="s">"full"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Pill Button<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h2 id="advanced-examples">Advanced Examples</h2> <h3 id="call-to-action-button">Call-to-Action Button</h3> <div class="text-center"> <a id="button-62059f8d62052633590d3f60ec092595" href="https://cgm.uni-frankfurt.de/signup" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-primary-500 to-primary-600 hover:from-primary-600 hover:to-primary-700 active:from-primary-700 active:to-primary-800 text-white shadow-lg shadow-primary-500/25 hover:shadow-xl hover:shadow-primary-500/30 hover:-translate-y-0.5 hover:scale-[1.02] active:scale-[0.98] focus:ring-primary-500/50 px-6 py-3 text-lg rounded-lg" role="button" aria-label="Get Started Today" > <span class="flex-shrink-0"> <svg class="w-4 h-4" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M15.59 14.37q.159.666.16 1.38a6 6 0 0 1-6 6v-4.8m5.84-2.58a14.98 14.98 0 0 0 6.16-12.12A14.98 14.98 0 0 0 9.631 8.41m5.96 5.96a14.9 14.9 0 0 1-5.841 2.58m-.119-8.54a6 6 0 0 0-7.381 5.84h4.8m2.581-5.84a14.9 14.9 0 0 0-2.58 5.84m2.699 2.7q-.155.032-.311.06a15 15 0 0 1-2.448-2.448l.06-.312m-2.24 2.39a4.49 4.49 0 0 0-1.757 4.306q.341.054.696.054a4.5 4.5 0 0 0 3.61-1.812M16.5 9a1.5 1.5 0 1 1-3 0a1.5 1.5 0 0 1 3 0"/></svg> </span> <span>Get Started Today</span> </a> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"/signup"</span><span class="w"> </span><span class="nx">style</span><span class="o">=</span><span class="s">"primary"</span><span class="w"> </span><span class="nx">size</span><span class="o">=</span><span class="s">"lg"</span><span class="w"> </span><span class="nx">align</span><span class="o">=</span><span class="s">"center"</span><span class="w"> </span><span class="nx">icon</span><span class="o">=</span><span class="s">"rocket-launch"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Get Started Today<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h3 id="external-link-with-new-tab">External Link with New Tab</h3> <div class="text-left"> <a id="button-2cb1bb8bbb2590cc46a8ead690d2da77" href="https://github.com/hugo-blox/kit" target="_blank" rel="noopener noreferrer" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-white dark:bg-zinc-900 border-2 border-primary-500 text-primary-600 dark:text-primary-400 hover:bg-primary-50 dark:hover:bg-primary-950/50 hover:border-primary-600 active:bg-primary-100 dark:active:bg-primary-950 shadow-md hover:shadow-lg hover:scale-105 active:scale-95 focus:ring-primary-500/50 px-4 py-2 text-base rounded-lg" role="button" aria-label="View on GitHub" > <span>View on GitHub</span> <span class="flex-shrink-0"> <svg class="w-4 h-4" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M13.5 6H5.25A2.25 2.25 0 0 0 3 8.25v10.5A2.25 2.25 0 0 0 5.25 21h10.5A2.25 2.25 0 0 0 18 18.75V10.5m-10.5 6L21 3m0 0h-5.25M21 3v5.25"/></svg> </span> </a> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"https://github.com/hugo-blox/kit"</span><span class="w"> </span><span class="nx">new_tab</span><span class="o">=</span><span class="s">"true"</span><span class="w"> </span><span class="nx">style</span><span class="o">=</span><span class="s">"outline"</span><span class="w"> </span><span class="nx">icon</span><span class="o">=</span><span class="s">"arrow-top-right-on-square"</span><span class="w"> </span><span class="nx">icon_position</span><span class="o">=</span><span class="s">"right"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>View on GitHub<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h3 id="download-button">Download Button</h3> <div class="text-left"> <a id="button-72ec86801f391f16b84b269ade9d2995" href="https://cgm.uni-frankfurt.de/files/document.pdf" class="inline-flex items-center gap-2 font-medium no-underline transition-all duration-300 ease-out transform-gpu focus:outline-none focus:ring-4 focus:ring-offset-2 focus:ring-offset-white dark:focus:ring-offset-zinc-900 disabled:opacity-50 disabled:cursor-not-allowed disabled:pointer-events-none bg-gradient-to-br from-secondary-500 to-secondary-600 hover:from-secondary-600 hover:to-secondary-700 active:from-secondary-700 active:to-secondary-800 text-white shadow-lg shadow-secondary-500/25 hover:shadow-xl hover:shadow-secondary-500/30 hover:scale-105 active:scale-95 focus:ring-secondary-500/50 px-4 py-2 text-base rounded-full" role="button" aria-label="Download PDF" > <span class="flex-shrink-0"> <svg class="w-4 h-4" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M19.5 14.25v-2.625a3.375 3.375 0 0 0-3.375-3.375h-1.5A1.125 1.125 0 0 1 13.5 7.125v-1.5a3.375 3.375 0 0 0-3.375-3.375H8.25m.75 12l3 3m0 0l3-3m-3 3v-6m-1.5-9H5.625c-.621 0-1.125.504-1.125 1.125v17.25c0 .621.504 1.125 1.125 1.125h12.75c.621 0 1.125-.504 1.125-1.125V11.25a9 9 0 0 0-9-9"/></svg> </span> <span>Download PDF</span> </a> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-go-html-template" data-lang="go-html-template"><span class="line"><span class="cl"><span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="nx">button</span><span class="w"> </span><span class="nx">url</span><span class="o">=</span><span class="s">"/files/document.pdf"</span><span class="w"> </span><span class="nx">style</span><span class="o">=</span><span class="s">"secondary"</span><span class="w"> </span><span class="nx">icon</span><span class="o">=</span><span class="s">"document-arrow-down"</span><span class="w"> </span><span class="nx">rounded</span><span class="o">=</span><span class="s">"full"</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span>Download PDF<span class="cp">{{</span><span class="err"><</span><span class="w"> </span><span class="err">/</span><span class="nx">button</span><span class="w"> </span><span class="err">></span><span class="cp">}}</span> </span></span></code></pre></div><h2 id="parameters">Parameters</h2> <table> <thead> <tr> <th>Parameter</th> <th>Type</th> <th>Default</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td><code>url</code></td> <td>string</td> <td><code>#</code></td> <td><strong>Required.</strong> Button destination URL (internal or external)</td> </tr> <tr> <td><code>text</code></td> <td>string</td> <td>Inner content</td> <td>Button text (overrides shortcode content)</td> </tr> <tr> <td><code>new_tab</code></td> <td>boolean</td> <td><code>false</code></td> <td>Whether to open link in new tab</td> </tr> <tr> <td><code>style</code></td> <td>string</td> <td><code>primary</code></td> <td>Button style: <code>primary</code>, <code>secondary</code>, <code>outline</code>, <code>ghost</code></td> </tr> <tr> <td><code>size</code></td> <td>string</td> <td><code>md</code></td> <td>Button size: <code>sm</code>, <code>md</code>, <code>lg</code>, <code>xl</code></td> </tr> <tr> <td><code>align</code></td> <td>string</td> <td><code>left</code></td> <td>Button alignment: <code>left</code>, <code>center</code>, <code>right</code></td> </tr> <tr> <td><code>icon</code></td> <td>string</td> <td>-</td> <td>Icon name from </td> </tr> <tr> <td><code>icon_position</code></td> <td>string</td> <td><code>left</code></td> <td>Icon position: <code>left</code>, <code>right</code></td> </tr> <tr> <td><code>rounded</code></td> <td>string</td> <td><code>md</code></td> <td>Border radius: <code>sm</code>, <code>md</code>, <code>lg</code>, <code>xl</code>, <code>full</code></td> </tr> <tr> <td><code>disabled</code></td> <td>boolean</td> <td><code>false</code></td> <td>Whether button should be disabled</td> </tr> </tbody> </table> <h2 id="security-features">Security Features</h2> <p>The button shortcode automatically handles security for external links:</p> <ul> <li><strong>External links</strong> get <code>rel="noreferrer"</code> attribute</li> <li><strong>External links opening in new tab</strong> get <code>rel="noopener noreferrer"</code></li> <li><strong>Internal links opening in new tab</strong> get <code>rel="noopener"</code></li> </ul> <p>This ensures safe navigation while maintaining functionality.</p> <h2 id="accessibility">Accessibility</h2> <p>The button shortcode includes built-in accessibility features:</p> <ul> <li>Proper <code>role="button"</code> attribute</li> <li><code>aria-label</code> support</li> <li>Keyboard focus indicators</li> <li>High contrast focus rings</li> <li>Disabled state handling</li> </ul> </article> <article> <h1>Callouts</h1> <p>Mon, 01 Jan 0001 00:00:00 +0000</p> <p>Hugo Blox supports GitHub and Obsidian-style Markdown callouts for maximum compatibility and content portability.</p> <p>Callouts are a useful feature to draw attention to important or related content such as notes, hints, or warnings in your articles.</p> <h2 id="usage">Usage</h2> <h3 id="basic-callout-types">Basic Callout Types</h3> <p>Hugo Blox supports all 15+ callout types from :</p> <p><strong>Information & Notes:</strong></p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!NOTE] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">This is a note callout with important information that users should know. </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-blue-100 dark:bg-blue-900 border-blue-500" data-callout="note" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-blue-600 dark:text-blue-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="m16.862 4.487l1.687-1.688a1.875 1.875 0 1 1 2.652 2.652L6.832 19.82a4.5 4.5 0 0 1-1.897 1.13l-2.685.8l.8-2.685a4.5 4.5 0 0 1 1.13-1.897zm0 0L19.5 7.125"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Note</div> <div class="callout-body"><p>This is a note callout with important information that users should know.</p></div> </div> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!INFO] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">Alternative info callout - same styling as NOTE. </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-blue-100 dark:bg-blue-900 border-blue-500" data-callout="info" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-blue-600 dark:text-blue-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="m11.25 11.25l.041-.02a.75.75 0 0 1 1.063.852l-.708 2.836a.75.75 0 0 0 1.063.853l.041-.021M21 12a9 9 0 1 1-18 0a9 9 0 0 1 18 0m-9-3.75h.008v.008H12z"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Info</div> <div class="callout-body"><p>Alternative info callout - same styling as NOTE.</p></div> </div> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!ABSTRACT] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">Use for abstracts, summaries, or TL;DR sections. </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-cyan-100 dark:bg-cyan-900 border-cyan-500" data-callout="abstract" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-cyan-600 dark:text-cyan-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M9 12h3.75M9 15h3.75M9 18h3.75m3 .75H18a2.25 2.25 0 0 0 2.25-2.25V6.108c0-1.135-.845-2.098-1.976-2.192a48 48 0 0 0-1.123-.08m-5.801 0q-.099.316-.1.664c0 .414.336.75.75.75h4.5a.75.75 0 0 0 .75-.75a2.3 2.3 0 0 0-.1-.664m-5.8 0A2.25 2.25 0 0 1 13.5 2.25H15a2.25 2.25 0 0 1 2.15 1.586m-5.8 0q-.563.035-1.124.08C9.095 4.01 8.25 4.973 8.25 6.108V8.25m0 0H4.875c-.621 0-1.125.504-1.125 1.125v11.25c0 .621.504 1.125 1.125 1.125h9.75c.621 0 1.125-.504 1.125-1.125V9.375c0-.621-.504-1.125-1.125-1.125zM6.75 12h.008v.008H6.75zm0 3h.008v.008H6.75zm0 3h.008v.008H6.75z"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Abstract</div> <div class="callout-body"><p>Use for abstracts, summaries, or TL;DR sections.</p></div> </div> </div> <p><strong>Actions & Tasks:</strong></p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!TODO] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">This is something that needs to be done. </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-blue-100 dark:bg-blue-900 border-blue-500" data-callout="todo" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-blue-600 dark:text-blue-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M9 12.75L11.25 15L15 9.75M21 12a9 9 0 1 1-18 0a9 9 0 0 1 18 0"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Todo</div> <div class="callout-body"><p>This is something that needs to be done.</p></div> </div> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!TIP] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">Here's a helpful tip to make your workflow more efficient! </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-emerald-100 dark:bg-emerald-900 border-emerald-500" data-callout="tip" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-emerald-600 dark:text-emerald-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M12 18v-5.25m0 0a6 6 0 0 0 1.5-.189m-1.5.189a6 6 0 0 1-1.5-.189m3.75 7.478a12.1 12.1 0 0 1-4.5 0m3.75 2.383a14.4 14.4 0 0 1-3 0M14.25 18v-.192c0-.983.658-1.823 1.508-2.316a7.5 7.5 0 1 0-7.517 0c.85.493 1.509 1.333 1.509 2.316V18"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Tip</div> <div class="callout-body"><p>Here’s a helpful tip to make your workflow more efficient!</p></div> </div> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!SUCCESS] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">Great job! This operation completed successfully. </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-green-100 dark:bg-green-900 border-green-500" data-callout="success" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-green-600 dark:text-green-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M9 12.75L11.25 15L15 9.75M21 12a9 9 0 1 1-18 0a9 9 0 0 1 18 0"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Success</div> <div class="callout-body"><p>Great job! This operation completed successfully.</p></div> </div> </div> <p><strong>Questions & Interactive:</strong></p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!QUESTION] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">What do you think about this approach? Let us know! </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-yellow-100 dark:bg-yellow-900 border-yellow-500" data-callout="question" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-yellow-700 dark:text-yellow-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M9.879 7.519c1.172-1.025 3.071-1.025 4.243 0c1.171 1.025 1.171 2.687 0 3.712q-.308.268-.67.442c-.746.361-1.452.999-1.452 1.827v.75M21 12a9 9 0 1 1-18 0a9 9 0 0 1 18 0m-9 5.25h.008v.008H12z"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Question</div> <div class="callout-body"><p>What do you think about this approach? Let us know!</p></div> </div> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!EXAMPLE] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">Here's a practical example of how to implement this feature. </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-purple-100 dark:bg-purple-900 border-purple-500" data-callout="example" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-purple-600 dark:text-purple-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M9.75 3.104v5.714a2.25 2.25 0 0 1-.659 1.591L5 14.5M9.75 3.104q-.376.034-.75.082m.75-.082a24.3 24.3 0 0 1 4.5 0m0 0v5.714c0 .597.237 1.17.659 1.591L19.8 15.3M14.25 3.104q.377.034.75.082M19.8 15.3l-1.57.393A9.07 9.07 0 0 1 12 15a9.07 9.07 0 0 0-6.23-.693L5 14.5m14.8.8l1.402 1.402c1.232 1.232.65 3.318-1.067 3.611A48.3 48.3 0 0 1 12 21a48 48 0 0 1-8.135-.687c-1.718-.293-2.3-2.379-1.067-3.61L5 14.5"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Example</div> <div class="callout-body"><p>Here’s a practical example of how to implement this feature.</p></div> </div> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!QUOTE] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">"The best way to predict the future is to invent it." - Alan Kay </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-gray-100 dark:bg-gray-800 border-gray-500" data-callout="quote" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-gray-600 dark:text-gray-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M20.25 8.511c.884.284 1.5 1.128 1.5 2.097v4.286c0 1.136-.847 2.1-1.98 2.193q-.51.041-1.02.072v3.091l-3-3q-2.031 0-4.02-.163a2.1 2.1 0 0 1-.825-.242m9.345-8.334a2 2 0 0 0-.476-.095a48.6 48.6 0 0 0-8.048 0c-1.131.094-1.976 1.057-1.976 2.192v4.286c0 .837.46 1.58 1.155 1.951m9.345-8.334V6.637c0-1.621-1.152-3.026-2.76-3.235A48.5 48.5 0 0 0 11.25 3c-2.115 0-4.198.137-6.24.402c-1.608.209-2.76 1.614-2.76 3.235v6.226c0 1.621 1.152 3.026 2.76 3.235q.865.113 1.74.194V21l4.155-4.155"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Quote</div> <div class="callout-body"><p>“The best way to predict the future is to invent it.” - Alan Kay</p></div> </div> </div> <p><strong>Warnings & Errors:</strong></p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!WARNING] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">Be careful! This action might have unexpected consequences. </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-orange-100 dark:bg-orange-900 border-orange-500" data-callout="warning" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-orange-600 dark:text-orange-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M12 9v3.75m-9.303 3.376c-.866 1.5.217 3.374 1.948 3.374h14.71c1.73 0 2.813-1.874 1.948-3.374L13.949 3.378c-.866-1.5-3.032-1.5-3.898 0zM12 15.75h.007v.008H12z"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Warning</div> <div class="callout-body"><p>Be careful! This action might have unexpected consequences.</p></div> </div> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!CAUTION] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">Danger! This operation is irreversible and could cause data loss. </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-red-100 dark:bg-red-900 border-red-500" data-callout="caution" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-red-600 dark:text-red-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M12 9v3.75m-9.303 3.376c-.866 1.5.217 3.374 1.948 3.374h14.71c1.73 0 2.813-1.874 1.948-3.374L13.949 3.378c-.866-1.5-3.032-1.5-3.898 0zM12 15.75h.007v.008H12z"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Caution</div> <div class="callout-body"><p>Danger! This operation is irreversible and could cause data loss.</p></div> </div> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!IMPORTANT] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">This is critical information that users must understand to proceed. </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-purple-100 dark:bg-purple-900 border-purple-500" data-callout="important" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-purple-600 dark:text-purple-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M12 9v3.75m9-.75a9 9 0 1 1-18 0a9 9 0 0 1 18 0m-9 3.75h.008v.008H12z"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Important</div> <div class="callout-body"><p>This is critical information that users must understand to proceed.</p></div> </div> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!DANGER] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">This is extremely dangerous - proceed with extreme caution! </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-red-100 dark:bg-red-900 border-red-500" data-callout="danger" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-red-600 dark:text-red-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M12 9v3.75m-9.303 3.376c-.866 1.5.217 3.374 1.948 3.374h14.71c1.73 0 2.813-1.874 1.948-3.374L13.949 3.378c-.866-1.5-3.032-1.5-3.898 0zM12 15.75h.007v.008H12z"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Danger</div> <div class="callout-body"><p>This is extremely dangerous - proceed with extreme caution!</p></div> </div> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!FAILURE] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">This operation failed. Check your configuration and try again. </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-red-100 dark:bg-red-900 border-red-500" data-callout="failure" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-red-600 dark:text-red-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="m9.75 9.75l4.5 4.5m0-4.5l-4.5 4.5M21 12a9 9 0 1 1-18 0a9 9 0 0 1 18 0"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Failure</div> <div class="callout-body"><p>This operation failed. Check your configuration and try again.</p></div> </div> </div> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!BUG] </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">Known issue: This feature doesn't work properly in Safari < 14. </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-red-100 dark:bg-red-900 border-red-500" data-callout="bug" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-red-600 dark:text-red-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M12 12.75q1.724 0 3.383.237c1.037.146 1.866.966 1.866 2.013c0 3.728-2.35 6.75-5.25 6.75S6.75 18.728 6.75 15c0-1.046.83-1.867 1.866-2.013A24 24 0 0 1 12 12.75m0 0c2.883 0 5.647.508 8.208 1.44a24 24 0 0 1-1.153 6.06M12 12.75c-2.883 0-5.647.508-8.208 1.44c.125 2.105.52 4.136 1.153 6.06M12 12.75a2.25 2.25 0 0 0 2.248-2.354M12 12.75a2.25 2.25 0 0 1-2.248-2.354M12 8.25q1.494-.001 2.922-.236c.403-.066.74-.358.795-.762a3.8 3.8 0 0 0-.399-2.25M12 8.25q-1.493-.001-2.922-.236c-.402-.066-.74-.358-.795-.762a3.73 3.73 0 0 1 .4-2.253M12 8.25a2.25 2.25 0 0 0-2.248 2.146M12 8.25a2.25 2.25 0 0 1 2.248 2.146M8.683 5a6 6 0 0 1-1.155-1.002c.07-.63.27-1.222.574-1.747M8.683 5a3.75 3.75 0 0 1 6.635 0m0 0c.427-.283.815-.62 1.155-.999a4.5 4.5 0 0 0-.575-1.752M4.921 6a24 24 0 0 0-.392 3.314a24 24 0 0 0 5.223 1.082M19.08 6q.308 1.622.392 3.314a24 24 0 0 1-5.223 1.082"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Bug</div> <div class="callout-body"><p>Known issue: This feature doesn’t work properly in Safari < 14.</p></div> </div> </div> <h3 id="custom-titles">Custom Titles</h3> <p>You can customize the title of any callout:</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl"><span class="k">> </span><span class="ge">[!WARNING]+ Custom Warning Title </span></span></span><span class="line"><span class="cl"><span class="k">> </span><span class="ge">This warning has a custom title instead of just "Warning". </span></span></span></code></pre></div> <div class="callout flex px-4 py-3 mb-6 rounded-md border-l-4 bg-orange-100 dark:bg-orange-900 border-orange-500" data-callout="warning" data-callout-metadata=""> <span class="callout-icon pr-3 pt-1 text-orange-600 dark:text-orange-300"> <svg height="24" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M12 9v3.75m-9.303 3.376c-.866 1.5.217 3.374 1.948 3.374h14.71c1.73 0 2.813-1.874 1.948-3.374L13.949 3.378c-.866-1.5-3.032-1.5-3.898 0zM12 15.75h.007v.008H12z"/></svg> </span> <div class="callout-content dark:text-neutral-300"> <div class="callout-title font-semibold mb-1">Custom Warning Title<br></div> <div class="callout-body"><p>This warning has a custom title instead of just “Warning”.</p></div> </div> </div> <h3 id="legacy-syntax-deprecated">Legacy Syntax (Deprecated)</h3> <p>The old shortcode syntax still works but shows a deprecation warning:</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-markdown" data-lang="markdown"><span class="line"><span class="cl">{{< callout note >}} </span></span><span class="line"><span class="cl">This still works but is deprecated. Use the Markdown syntax above! </span></span><span class="line"><span class="cl">{{< /callout >}} </span></span></code></pre></div><h3 id="css-customization">CSS Customization</h3> <p>Hugo Blox generates callouts with semantic CSS classes and data attributes, making customization easy. Each callout has:</p> <ul> <li>Base class: <code>.callout</code></li> <li>Type-specific data attribute: <code>data-callout="note"</code></li> <li>Component classes: <code>.callout-icon</code>, <code>.callout-title</code>, <code>.callout-content</code>, <code>.callout-body</code></li> </ul> <p><strong>Custom CSS Example</strong> (add to your <code>assets/css/custom.css</code>):</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-css" data-lang="css"><span class="line"><span class="cl"><span class="c">/* Customize NOTE callouts */</span> </span></span><span class="line"><span class="cl"><span class="p">.</span><span class="nc">callout</span><span class="o">[</span><span class="nt">data-callout</span><span class="o">=</span><span class="s2">"note"</span><span class="o">]</span> <span class="p">{</span> </span></span><span class="line"><span class="cl"> <span class="k">border-left-width</span><span class="p">:</span> <span class="mi">8</span><span class="kt">px</span><span class="p">;</span> </span></span><span class="line"><span class="cl"> <span class="k">box-shadow</span><span class="p">:</span> <span class="mi">0</span> <span class="mi">4</span><span class="kt">px</span> <span class="mi">6</span><span class="kt">px</span> <span class="mi">-1</span><span class="kt">px</span> <span class="nb">rgb</span><span class="p">(</span><span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="o">/</span> <span class="mf">0.1</span><span class="p">);</span> </span></span><span class="line"><span class="cl"><span class="p">}</span> </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl"><span class="c">/* Make SUCCESS callouts pulse */</span> </span></span><span class="line"><span class="cl"><span class="p">.</span><span class="nc">callout</span><span class="o">[</span><span class="nt">data-callout</span><span class="o">=</span><span class="s2">"success"</span><span class="o">]</span> <span class="p">{</span> </span></span><span class="line"><span class="cl"> <span class="k">animation</span><span class="p">:</span> <span class="n">pulse</span> <span class="mi">2</span><span class="kt">s</span> <span class="kc">infinite</span><span class="p">;</span> </span></span><span class="line"><span class="cl"><span class="p">}</span> </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl"><span class="c">/* Custom icon styling */</span> </span></span><span class="line"><span class="cl"><span class="p">.</span><span class="nc">callout-icon</span> <span class="nt">svg</span> <span class="p">{</span> </span></span><span class="line"><span class="cl"> <span class="k">transition</span><span class="p">:</span> <span class="k">transform</span> <span class="mf">0.2</span><span class="kt">s</span><span class="p">;</span> </span></span><span class="line"><span class="cl"><span class="p">}</span> </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl"><span class="p">.</span><span class="nc">callout</span><span class="p">:</span><span class="nd">hover</span> <span class="p">.</span><span class="nc">callout-icon</span> <span class="nt">svg</span> <span class="p">{</span> </span></span><span class="line"><span class="cl"> <span class="k">transform</span><span class="p">:</span> <span class="nb">scale</span><span class="p">(</span><span class="mf">1.1</span><span class="p">);</span> </span></span><span class="line"><span class="cl"><span class="p">}</span> </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl"><span class="c">/* Dark mode overrides */</span> </span></span><span class="line"><span class="cl"><span class="p">@</span><span class="k">media</span> <span class="o">(</span><span class="nt">prefers-color-scheme</span><span class="o">:</span> <span class="nt">dark</span><span class="o">)</span> <span class="p">{</span> </span></span><span class="line"><span class="cl"> <span class="p">.</span><span class="nc">callout</span><span class="o">[</span><span class="nt">data-callout</span><span class="o">=</span><span class="s2">"warning"</span><span class="o">]</span> <span class="p">{</span> </span></span><span class="line"><span class="cl"> <span class="k">background-color</span><span class="p">:</span> <span class="nb">rgb</span><span class="p">(</span><span class="mi">92</span> <span class="mi">25</span> <span class="mi">2</span><span class="p">);</span> </span></span><span class="line"><span class="cl"> <span class="k">border-color</span><span class="p">:</span> <span class="nb">rgb</span><span class="p">(</span><span class="mi">245</span> <span class="mi">158</span> <span class="mi">11</span><span class="p">);</span> </span></span><span class="line"><span class="cl"> <span class="p">}</span> </span></span><span class="line"><span class="cl"><span class="p">}</span> </span></span></code></pre></div><p>This approach matches , ensuring your styles work across platforms.</p> <h3 id="benefits-of-the-new-syntax">Benefits of the New Syntax</h3> <ul> <li><strong>Portable</strong>: Works with GitHub, Obsidian, and other Markdown editors</li> <li><strong>Standard</strong>: Uses widely-adopted Markdown callout syntax</li> <li><strong>Clean</strong>: No Hugo-specific shortcodes needed</li> <li><strong>Future-proof</strong>: Supported by the latest Hugo versions (0.132.0+)</li> <li><strong>Customizable</strong>: Semantic CSS classes and data attributes for easy styling</li> <li><strong>Complete</strong>: All 15+ Obsidian callout types supported</li> <li><strong>Multilingual</strong>: Callout titles are automatically translated based on your site’s language (and can be customized in the language packs)</li> </ul> </article> <article> <h1>Cards</h1> <p>Mon, 01 Jan 0001 00:00:00 +0000</p> <p>A Hugo extension to create cards. Cards can be shown as links or as plain text.</p> <h2 id="usage">Usage</h2> <div class="hb-cards mt-4 grid gap-4 not-prose" style="--hb-cols: 1;"> <a class="hb-card group"href="../" > <span class="hb-card-title p-4"> <svg style="height: 1em; width: 1em;" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path fill="none" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" d="M4.26 10.147a60 60 0 0 0-.491 6.347A48.6 48.6 0 0 1 12 20.904a48.6 48.6 0 0 1 8.232-4.41a61 61 0 0 0-.491-6.347m-15.482 0a51 51 0 0 0-2.658-.813A60 60 0 0 1 12 3.493a60 60 0 0 1 10.399 5.84q-1.345.372-2.658.814m-15.482 0A51 51 0 0 1 12 13.489a50.7 50.7 0 0 1 7.74-3.342M6.75 15a.75.75 0 1 0 0-1.5a.75.75 0 0 0 0 1.5m0 0v-3.675A55 55 0 0 1 12 8.443m-7.007 11.55A5.98 5.98 0 0 0 6.75 15.75v-1.5"/></svg>Learn Shortcodes</span></a> <a class="hb-card group"> <span class="hb-card-title p-4">A card without an icon or link</span></a> </div> <p>is rendered by:</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-fallback" data-lang="fallback"><span class="line"><span class="cl">{{< cards >}} </span></span><span class="line"><span class="cl"> {{< card url="../callout" title="Callout" icon="academic-cap" >}} </span></span><span class="line"><span class="cl"> {{< card url="" title="A card without an icon" >}} </span></span><span class="line"><span class="cl">{{< /cards >}} </span></span></code></pre></div><h2 id="options">Options</h2> <table> <thead> <tr> <th>Parameter</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td><code>icon</code></td> <td>Name of the icon. Defaults to </td> </tr> <tr> <td><code>title</code></td> <td>Title heading for the card.</td> </tr> <tr> <td><code>subtitle</code></td> <td>Subtitle heading (supports Markdown).</td> </tr> <tr> <td><code>url</code></td> <td>URL</td> </tr> </tbody> </table> </article> <article> <h1>Internationalization (i18n)</h1> <p>Mon, 01 Jan 0001 00:00:00 +0000</p> <p>Hugo Blox enables you to easily edit the interface text as well as translating your site into multiple languages using Hugo’s feature.</p> <p>View the full docs at </p> </article> <article> <h1>Spoilers</h1> <p>Mon, 01 Jan 0001 00:00:00 +0000</p> <p>A Hugo shortcode to toggle collapsible content.</p> <h2 id="example">Example</h2> <details class="spoiler " id="spoiler-0"> <summary class="cursor-pointer">Click to view the spoiler</summary> <div class="rounded-lg bg-neutral-50 dark:bg-neutral-800 p-2"> <p>You found me!</p> <p>Markdown is <strong>supported</strong>.</p> </div> </details> <h2 id="usage">Usage</h2> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-fallback" data-lang="fallback"><span class="line"><span class="cl">{{< spoiler text="Click to view the spoiler" >}} </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl">This is the content of the details. </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl">Markdown is **supported**. </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl">{{< /spoiler >}} </span></span></code></pre></div> </article> <article> <h1>Steps</h1> <p>Mon, 01 Jan 0001 00:00:00 +0000</p> <p>Display a series of steps, such as for a tutorial.</p> <h2 id="example">Example</h2> <div class="hb-steps"> <h3 id="step-1">Step 1</h3> <p>The first step here…</p> <h3 id="step-2">Step 2</h3> <p>The second step here…</p> <h3 id="step-3">Step 3</h3> <p>The third step here…</p> </div> <h2 id="usage">Usage</h2> <p>Use the Markdown level-3 headings to represent step titles within the <code>steps</code> shortcode:</p> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-fallback" data-lang="fallback"><span class="line"><span class="cl">{{% steps %}} </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl">### Step 1 </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl">The first step here... </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl">### Step 2 </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl">The second step here... </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl">### Step 3 </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl">The third step here... </span></span><span class="line"><span class="cl"> </span></span><span class="line"><span class="cl">{{% /steps %}} </span></span></code></pre></div> </article> </main></body></html>