peak-calling
Perform peak calling for ChIP-seq or ATAC-seq data using MACS2, with intelligent parameter detection from user feedback. Use it when you want to call peaks for ChIP-seq data or ATAC-seq data.
npx skills add majiayu000/claude-skill-registry --skill 3-peak-calling --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.
# Peak Calling ## Overview This skill automatically performs core **peak calling** with **MACS2** for **ChIP-seq** and **ATAC-seq** data, based on the BAM files in the current directory. It includes automatic experiment recognition and parameter selection. Main steps include: - Refer to the **Inputs & Outputs** section to check inputs and build the output architecture. All the output file should located in `${proj_dir}` in Step 0. - **Always prompt user** for `genome_size` to use (e.g. hs or mm). **Never decide by yourself**. - **Always prompt user** if required control files are missing for ChIP-seq data. - **Detect experiment type** (TF, histone mark, or ATAC-seq). - **Automatically decide** whether to call narrow or broad peaks. - Always use filtered BAM file (`filtered.bam`) if available. - **Detect sequencing type** (single-end or paired-end) using SAM/BAM flags. - **Perform MACS2 peak calling** accordingly. - **Generate a parameter log file** (`${sample}_used_parameters.txt`) with justification for each chosen option. --- ## Inputs & Outputs ### Inputs ```bash ${sample}.bam # filtered bam files ``` ### Outputs ```bash all_peak_calling/ peaks/ ${sample}.narrowPeak # or ${sampl
- Overview
- Inputs & Outputs
- Inputs
- Outputs
- Decision Tree
- Step 0: Initialize Project
- Step 1. Identify and Classify BAM Files
- Step 2. Detect Sequencing Type (Single-End or Paired-End)
- Step 3. Detect Experiment Type and Choose Peak Mode
- Step 4. Execute MACS2 with Auto Parameters
- Step 5. Generate Parameter Log File
all_peak_calling/ peaks/ temp/ logs/ find . -name "*.bam" | sort samtools flagstat sample.bam | egrep "properly paired|singletons"
What does the peak-calling skill do?
Perform peak calling for ChIP-seq or ATAC-seq data using MACS2, with intelligent parameter detection from user feedback. Use it when you want to call peaks for ChIP-seq data or ATAC-seq data.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 3-peak-calling --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.