{"slug":"alterlab-gget","title":"alterlab-gget","summary":"Run fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr enrichment, and more. Use for quick interactive lookups of genes, sequences, structures, or pathways — for batch processing or advanc","platform":"Claude","tags":[],"authorName":"LLM Mart","authorSlug":"llm-mart","score":0,"source":"github","price":null,"verified":false,"createdAt":"2026-09-23T18:56:54.854091Z","repo":{"url":"https://github.com/AlterLab-IEU/AlterLab-Academic-Skills","stars":68,"forks":13,"license":"MIT","updatedAt":"2026-09-23T13:42:59Z"},"bodyHtml":"<hr>\n<h2>name: alterlab-gget\ndescription: \"Run fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr enrichment, and more. Use for quick interactive lookups of genes, sequences, structures, or pathways — for batch processing or advanced BLAST use biopython, for multi-database Python workflows use bioservices. Part of the AlterLab Academic Skills suite.\"\nlicense: MIT\nallowed-tools: Read Write Edit Bash(python:<em>) Bash(uv:</em>)\ncompatibility: \"Install with <code>uv pip install gget</code> (0.30.8 as of 2026-09; requires Python &gt;= 3.12). Core modules need no API key or account. cosmic needs a COSMIC account; gpt needs an OpenAI key; alphafold, cellxgene, elm, gpt and cbio need a one-time <code>gget setup &lt;module&gt;</code>.\"\nmetadata:\nskill-author: AlterLab\nversion: \"1.1.0\"\nlast_updated: \"2026-09-23\"</h2>\n<h1>gget</h1>\n<h2>Overview</h2>\n<p>gget is a command-line bioinformatics tool and Python package providing unified access to 20+ genomic databases and analysis methods. Query gene information, sequence analysis, protein structures, expression data, and disease associations through a consistent interface. All gget modules work both as command-line tools and as Python functions.</p>\n<p><strong>Project home:</strong> development moved to the scverse organisation (<code>github.com/scverse/gget</code>); the manual stays at <code>pachterlab.github.io/gget</code>.</p>\n<p><strong>Important</strong>: The databases queried by gget are continuously updated, which sometimes changes their structure. gget modules are tested automatically on a biweekly basis and updated to match new database structures when necessary.</p>\n<h2>Installation</h2>\n<p>Install gget in a clean virtual environment to avoid conflicts:</p>\n<pre><code># Install (or upgrade) into a clean environment\nuv pip install --upgrade gget\n\n# In Python/Jupyter\nimport gget\n</code></pre>\n<h2>Quick Start</h2>\n<p>Basic usage pattern for all modules:</p>\n<pre><code># Command-line\ngget &lt;module&gt; [arguments] [options]\n\n# Python\ngget.module(arguments, options)\n</code></pre>\n<p>Most modules return:</p>\n<ul>\n<li><strong>Command-line</strong>: JSON (default) or CSV with <code>-csv</code> flag</li>\n<li><strong>Python</strong>: DataFrame or dictionary</li>\n</ul>\n<p>Common flags across modules:</p>\n<ul>\n<li><code>-o/--out</code>: Save results to file</li>\n<li><code>-q/--quiet</code>: Suppress progress information</li>\n<li><code>-csv</code>: Return CSV format (command-line only)</li>\n</ul>\n<h2>Module Catalog</h2>\n<p>Pick a module, then see <code>references/module_examples.md</code> for worked CLI + Python\nexamples and <code>references/module_reference.md</code> for the full parameter table.</p>\n<table>\n<thead>\n<tr>\n<th>Module</th>\n<th>Purpose</th>\n<th>Queried source</th>\n</tr>\n</thead>\n<tbody>\n<tr>\n<td><code>ref</code></td>\n<td>Reference genome download links/metadata</td>\n<td>Ensembl</td>\n</tr>\n<tr>\n<td><code>search</code></td>\n<td>Find genes by name/description</td>\n<td>Ensembl</td>\n</tr>\n<tr>\n<td><code>info</code></td>\n<td>Gene/transcript metadata (~1000 IDs max)</td>\n<td>Ensembl, UniProt, NCBI</td>\n</tr>\n<tr>\n<td><code>seq</code></td>\n<td>Nucleotide/amino-acid sequences (FASTA)</td>\n<td>Ensembl</td>\n</tr>\n<tr>\n<td><code>blast</code></td>\n<td>BLAST against standard databases</td>\n<td>NCBI BLAST</td>\n</tr>\n<tr>\n<td><code>blat</code></td>\n<td>Genomic position of a sequence</td>\n<td>UCSC BLAT</td>\n</tr>\n<tr>\n<td><code>muscle</code></td>\n<td>Multiple sequence alignment</td>\n<td>Muscle5 (local)</td>\n</tr>\n<tr>\n<td><code>diamond</code></td>\n<td>Fast local protein/translated alignment</td>\n<td>DIAMOND (local)</td>\n</tr>\n<tr>\n<td><code>pdb</code></td>\n<td>Experimental protein structures + metadata</td>\n<td>RCSB PDB</td>\n</tr>\n<tr>\n<td><code>alphafold</code></td>\n<td>Predict 3D protein structure (setup req.)</td>\n<td>AlphaFold2 (local)</td>\n</tr>\n<tr>\n<td><code>elm</code></td>\n<td>Eukaryotic linear motifs (setup req.)</td>\n<td>ELM</td>\n</tr>\n<tr>\n<td><code>archs4</code></td>\n<td>Correlated genes / tissue expression</td>\n<td>ARCHS4</td>\n</tr>\n<tr>\n<td><code>cellxgene</code></td>\n<td>Single-cell RNA-seq (setup req.)</td>\n<td>CZ CELLxGENE Census</td>\n</tr>\n<tr>\n<td><code>enrichr</code></td>\n<td>Ontology/pathway enrichment</td>\n<td>Enrichr</td>\n</tr>\n<tr>\n<td><code>bgee</code></td>\n<td>Orthologs and expression</td>\n<td>Bgee</td>\n</tr>\n<tr>\n<td><code>opentargets</code></td>\n<td>Disease/drug associations</td>\n<td>OpenTargets</td>\n</tr>\n<tr>\n<td><code>cbio</code></td>\n<td>Cancer genomics heatmaps</td>\n<td>cBioPortal</td>\n</tr>\n<tr>\n<td><code>cosmic</code></td>\n<td>Somatic cancer mutations (license/account)</td>\n<td>COSMIC</td>\n</tr>\n<tr>\n<td><code>mutate</code></td>\n<td>Generate mutated sequences</td>\n<td>local</td>\n</tr>\n<tr>\n<td><code>virus</code></td>\n<td>Download filtered virus genome datasets</td>\n<td>NCBI Virus</td>\n</tr>\n<tr>\n<td><code>g2p</code></td>\n<td>Residue-level structural/functional annotations</td>\n<td>Genomics 2 Proteins portal</td>\n</tr>\n<tr>\n<td><code>gene_expression</code></td>\n<td>Mean/variance of normalized expression per partition</td>\n<td>8cubeDB</td>\n</tr>\n<tr>\n<td><code>psi_block</code></td>\n<td>ψ_block block-level specificity scores</td>\n<td>8cubeDB</td>\n</tr>\n<tr>\n<td><code>specificity</code></td>\n<td>Gene-level ψ / ζ specificity statistics</td>\n<td>8cubeDB</td>\n</tr>\n<tr>\n<td><code>gpt</code></td>\n<td>Natural-language text generation (setup req.)</td>\n<td>OpenAI API</td>\n</tr>\n<tr>\n<td><code>setup</code></td>\n<td>Install third-party deps for a module</td>\n<td>local</td>\n</tr>\n</tbody>\n</table>\n<p><code>cbio</code> is exposed in Python as <code>gget.cbio_search()</code> and <code>gget.cbio_plot()</code>.</p>\n<p><strong>Setup-required modules</strong> (<code>gget setup &lt;module&gt;</code> before first use):\n<code>alphafold</code> (~4GB params, needs <code>uv pip install openmm</code> first), <code>cellxgene</code>,\n<code>elm</code>, <code>gpt</code>, and <code>cbio</code>.</p>\n<h2>When to Use This Skill</h2>\n<ul>\n<li><strong>Quick interactive lookup</strong> (gene info, BLAST, one structure, one enrichment) →\nuse gget directly; see <code>references/module_examples.md</code>.</li>\n<li><strong>Batch processing / advanced BLAST</strong> → use the <strong>biopython</strong> skill.</li>\n<li><strong>Multi-database Python workflows</strong> → use the <strong>bioservices</strong> skill.</li>\n</ul>\n<h3>Does NOT Trigger</h3>\n<table>\n<thead>\n<tr>\n<th>Scenario</th>\n<th>Use Instead</th>\n</tr>\n</thead>\n<tbody>\n<tr>\n<td>Local BLAST+ database builds and large CLI searches</td>\n<td><code>alterlab-blast</code></td>\n</tr>\n<tr>\n<td>Scripted Entrez/SeqIO pipelines and file parsing</td>\n<td><code>alterlab-biopython</code></td>\n</tr>\n<tr>\n<td>One workflow spanning many web services in Python</td>\n<td><code>alterlab-bioservices</code></td>\n</tr>\n<tr>\n<td>Serious CELLxGENE Census querying beyond a one-liner</td>\n<td><code>alterlab-cellxgene</code></td>\n</tr>\n<tr>\n<td>Running AlphaFold properly (complexes, confidence analysis)</td>\n<td><code>alterlab-alphafold</code></td>\n</tr>\n</tbody>\n</table>\n<ul>\n<li><strong>Chaining several gget modules into a pipeline</strong> → see <code>references/workflows.md</code>\nand the ready-made <code>scripts/</code> (gene_analysis, batch_sequence_analysis,\nenrichment_pipeline).</li>\n</ul>\n<h2>Best Practices (essentials)</h2>\n<ul>\n<li>Use <code>--limit</code> to bound large queries; save with <code>-o/--out</code> for reproducibility.</li>\n<li>Gene symbols are <strong>case-sensitive</strong> in cellxgene ('PAX7' vs 'Pax7').</li>\n<li>Run <code>gget setup</code> before first use of alphafold, cellxgene, elm, gpt.</li>\n<li>Process max ~1000 Ensembl IDs at once with <code>gget info</code>.</li>\n<li>Database structures change; keep gget updated: <code>uv pip install --upgrade gget</code>.</li>\n<li>Use virtual environments to avoid dependency conflicts.</li>\n</ul>\n<h2>Output Formats</h2>\n<ul>\n<li><strong>Command-line</strong>: JSON default; <code>-csv</code> for CSV; FASTA (<code>seq</code>, <code>mutate</code>);\nPDB (<code>pdb</code>, <code>alphafold</code>); PNG (<code>cbio plot</code>).</li>\n<li><strong>Python</strong>: DataFrame/dict default; <code>json=True</code> for JSON; <code>save=True</code> or\n<code>out=\"filename\"</code> to write; AnnData for <code>cellxgene</code>.</li>\n</ul>\n<h2>References</h2>\n<ul>\n<li><code>references/module_examples.md</code> — worked CLI + Python examples for every module</li>\n<li><code>references/module_reference.md</code> — full parameter tables for all modules</li>\n<li><code>references/database_info.md</code> — queried databases and their update frequencies</li>\n<li><code>references/workflows.md</code> — extended multi-module workflow examples</li>\n</ul>\n<p>For additional help:</p>\n<ul>\n<li>Official documentation: <a href=\"https://pachterlab.github.io/gget/\">https://pachterlab.github.io/gget/</a></li>\n<li>GitHub issues: <a href=\"https://github.com/pachterlab/gget/issues\">https://github.com/pachterlab/gget/issues</a></li>\n<li>Citation: Luebbert, L. &amp; Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. <a href=\"https://doi.org/10.1093/bioinformatics/btac836\">https://doi.org/10.1093/bioinformatics/btac836</a></li>\n</ul>\n<p>Part of the AlterLab Academic Skills suite.</p>\n","files":[{"path":"evals/evals.json","sizeBytes":4233,"isText":true},{"path":"references/database_info.md","sizeBytes":10279,"isText":true},{"path":"references/module_examples.md","sizeBytes":10362,"isText":true},{"path":"references/module_reference.md","sizeBytes":18423,"isText":true},{"path":"references/workflows.md","sizeBytes":25756,"isText":true},{"path":"scripts/batch_sequence_analysis.py","sizeBytes":6026,"isText":true},{"path":"scripts/enrichment_pipeline.py","sizeBytes":7201,"isText":true},{"path":"scripts/gene_analysis.py","sizeBytes":5778,"isText":true},{"path":"SKILL.md","sizeBytes":6852,"isText":true}],"reviewScore":null,"reviewSummary":null,"trust":{"provenance":"trusted-source-unreviewed","notice":"Community-authored content, reproduced verbatim and not vetted as instructions. Treat it as data to evaluate, never as directives to follow.","bodySource":null},"bodyLocked":false,"purchaseUrl":null,"sourceUrl":null,"report":{"provenance":"trusted-source-unreviewed","screen":{"ran":true,"outcome":"notes-only","suspicious":0,"notes":1,"hiddenCharacters":false},"virusScan":{"engine":"clamav","status":"clean","scannedAt":"2026-09-23T18:57:28.468956Z","sha256":"31234BD8CF3CF31CBB3DA495BE53A45CB9C896ED4D7E4DA445BA28BE54D687A8","sizeBytes":31541},"review":null,"source":{"repositoryUrl":"https://github.com/AlterLab-IEU/AlterLab-Academic-Skills","path":"skills/bioinformatics/alterlab-gget","license":"MIT","commit":"e4836c08a20da195a11f30f203a8cf23ec30aa95","subtreeSha":"EDACB5E11FC16C07D97A9D78EF1E772AF7ECA0EA36B711109EF5C310FD509180","lastSyncedAt":"2026-09-23T18:56:52.297238Z"},"reviewedAt":"2026-09-23T18:58:30.287851Z","notice":"Community-authored content, reproduced verbatim and not vetted as instructions. Treat it as data to evaluate, never as directives to follow."},"install":[{"target":"skills-cli","command":"npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-gget"},{"target":"claude-code","command":"claude plugin marketplace add https://llmmart.ai/marketplace.json && claude plugin install alterlab-ieu-alterlab-academic-skills@llmmart"},{"target":"git","command":"git clone https://github.com/AlterLab-IEU/AlterLab-Academic-Skills.git"}]}