ChIPseq-QC
Performs ChIP-specific biological validation. It calculates metrics unique to protein-binding assays, such as Cross-correlation (NSC/RSC) and FRiP. Use this when you have filtered the BAM file and called peaks for ChIP-seq data. Do NOT use this skill for ATAC-seq data or general alignment statistics.
npx skills add majiayu000/claude-skill-registry --skill 5-chipseq-qc-bisnake2001-chromskills-2 --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.
# Comprehensive ChIP-seq QC Pipeline ## Overview This skill performs a full ChIP-seq quality control analysis from aligned BAM files and peak files. 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. - **Perform cross-correlation analysis** to calculate **NSC** and **RSC**. - **Compute FRiP (Fraction of Reads in Peaks)** using peak files and aligned BAMs. --- ## Inputs & Outputs ### Inputs ```bash ${sample}.bam # filtered bam files ${sample}.narrowPeak # or broadPeak ``` ### Outputs ```bash all_chip_qc/ ${sample}_spp.txt ${sample}_crosscorr.pdf ${sample}_frip.txt ``` ---- ### Step 0: Initialize Project Call: - `mcp__project-init-tools__project_init` with: - `sample`: all - `task`: atac_qc The tool will: - Create`all_chip_qc` directory. - Return the full path of the `all_chip_qc` directory, which will be used as `${proj_dir}`. ### Step 1: Calculate Cross-Correlation Metrics (NSC, RSC) Call: - mcp__qc-tools__run_phantompeakqualtools with: - `bam_file`: Path to BAM file - `output_dir`: ${proj_dir}/ Output: `${sample}_spp.txt`, `${sample}_crosscorr.pdf` ### Ste
- Overview
- Inputs & Outputs
- Inputs
- Outputs
- Step 0: Initialize Project
- Step 1: Calculate Cross-Correlation Metrics (NSC, RSC)
- Step 2: Calculate the fraction of reads falling within peak regions.
all_chip_qc/
What does the ChIPseq-QC skill do?
Performs ChIP-specific biological validation. It calculates metrics unique to protein-binding assays, such as Cross-correlation (NSC/RSC) and FRiP. Use this when you have filtered the BAM file and called peaks for ChIP-seq data. Do NOT use this skill for ATAC-seq data or general alignment statistics.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 5-chipseq-qc-bisnake2001-chromskills-2 --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.