functional-enrichment
Perform GO and KEGG functional enrichment using HOMER from genomic regions (BED/narrowPeak/broadPeak) or gene lists, and produce R-based barplot/dotplot visualizations. Use this skill when you want to perform GO and KEGG functional enrichment using HOMER from genomic regions or just want to link genomic region to genes.
npx skills add majiayu000/claude-skill-registry --skill 11-toolbased-functional-enrichment-bisnake2001-chromskills --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Functional Enrichment (HOMER + R) ## Overview - **Validate input**: Accept BED/peak files with genomic coordinates or gene lists; check format and genome assembly. - **Map regions to genes**: Convert regions to a unique gene set using HOMER `annotatePeaks.pl`. - **Run GO enrichment**: Use HOMER `findGO.pl` (or `annotatePeaks.pl -go`) for BP/MF/CC. - **Run KEGG enrichment**: Use HOMER `findGO.pl -kegg` (or `annotatePeaks.pl -kegg`). - **Collect outputs**: Save tidy tables for downstream plotting and a compact summary of top terms. - **Visualize in R**: Create barplots and dotplots (GO/KEGG) with `ggplot2` from standardized outputs. - **QC & troubleshooting**: Provide checks for genome mismatch, chromosome naming, and low-signal inputs. ## Inputs & Outputs ### Inputs (choose one): #### Option 1: Input is a genomic region file (BED/narrowPeak/broadPeak) Genomic region formats supported: - **BED files**: Standard genomic interval format - **narrowPeak**: narrow peak format - **broadPeak**: broad peak format #### Option 2: Input is a gene list (txt) - `gene_list.txt` with one official gene symbol per line (no header). And an optional `gene_list_background.txt` with one official gene s
- Overview
- Inputs & Outputs
- Inputs (choose one):
- Outputs (directory layout):
- Decision Tree
- Step 0 — Gather Required Information from the User
- Step 1: Initialize Project
- Step 2: Prepare genome file for homer
- Step 3 (Optional): Standardize chromosome names for BED files
- Step 4 (Optional): Convert gene ID to gene symbol
- Step 5: GO enrichment analysis
- Step 6: Visualization in Python (barplot & dotplot)
- Notes & Best Practices
- Troubleshooting
results/ biological_process.txt cellular_component.txt molecular_function.txt kegg.txt biocyc.txt chromosome.txt cosmic.txt interactions.txt interpro.txt
What does the functional-enrichment skill do?
Perform GO and KEGG functional enrichment using HOMER from genomic regions (BED/narrowPeak/broadPeak) or gene lists, and produce R-based barplot/dotplot visualizations. Use this skill when you want to perform GO and KEGG functional enrichment using HOMER from genomic regions or just want to link genomic region to genes.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 11-toolbased-functional-enrichment-bisnake2001-chromskills --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.