genomic-feature-annotation
This skill is used to perform genomic feature annotation and visualization for any file containing genomic region information using Homer (Hypergeometric Optimization of Motif EnRichment). It annotates regions such as promoters, exons, introns, intergenic regions, and TSS proximity, and generates visual summaries of feature distributions. ChIPseeker mode is also supported according to requirements.
npx skills add majiayu000/claude-skill-registry --skill 10-toolbased-genomic-feature-annotation-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.
# Genomic Feature Annotation and Visualization with Homer ## Overview - Prepare genomic region files in BED or other supported formats. Ensure that the input genomic regions are provided in a valid BED format (chromosome, start, end). If the file does not meet this format, extract the required columns to create a valid BED file.regions file. - Identify and specify the correct genome assembly for annotation. - Always prompt user for the tool to use, choose from ChIPseeker or HOMER - If the user choose HOMER, then: - Annotate the genomic regions using Homer's `annotatePeaks.pl`. - Generate annotation statistics and feature distribution summaries. - Visualize annotation results (e.g., pie charts, barplots). --- ## When to use this skill - Find target genes of a certain TF. This skill will return an annotated peak file with the nearby genes of the TF. Genes whose promoter annotated to the TF peaks could be candidate target genes of the TF. - Annotate the genomic regions like TF peaks, histone modification peaks, ATAC-seq peaks, etc. - Generate annotation statistics and feature distribution summaries. - Visualize annotation results (e.g., pie charts, barplots). --- ## Inputs & Outputs #
- Overview
- When to use this skill
- Inputs & Outputs
- Inputs
- Outputs
- Decision Tree
- Step 0 — Gather Required Information from the User
- Step 1: Initialize Project
- Step 2 (Optional): Standardize chromosome names for BED files
- Step 3: Genomic Feature Annotation
- Step 4: Visualize the annotation results (executed only in HOMER mode)
- Step 5. Interpretation of Results
- Best Practices
genomic_feature_annotation/ results/ logs/ plots/
What does the genomic-feature-annotation skill do?
This skill is used to perform genomic feature annotation and visualization for any file containing genomic region information using Homer (Hypergeometric Optimization of Motif EnRichment). It annotates regions such as promoters, exons, introns, intergenic regions, and TSS proximity, and generates visual summaries of feature distributions. ChIPseeker mode is also supported according to requirements.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 10-toolbased-genomic-feature-annotation-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.