Compute NSC/RSC cross-correlation and FRiP metrics from aligned BAMs and peak files.
npx skills add https://github.com/BIsnake2001/ChromSkills --skill chipseq-qc
Please help me install this Agent Skill. Skill: ChIPseq-QC Source: https://github.com/BIsnake2001/ChromSkills/tree/main/5.ChIPseq-QC Command: npx skills add https://github.com/BIsnake2001/ChromSkills --skill chipseq-qc
This skill provides QC metrics for ChIP-seq data by computing cross-correlation (NSC/RSC) and FRiP from aligned BAMs and called peaks, enabling assessment of ChIP data quality before downstream analysis.
Run this skill after peak calling to produce QC metrics for your ChIP-seq BAM and peak files.
High-intent search queries and answers about installing and using this skill.
You can calculate ChIP-seq cross-correlation metrics NSC and RSC by processing aligned BAM files to evaluate signal enrichment and data quality before downstream analysis.
FRiP computation estimates the fraction of reads within peak regions from aligned BAMs and called peak files, gauging ChIP-seq enrichment quality after peak calling.
Run ChIP-seq QC on filtered BAMs and peak files when high-quality assessment is required post-alignment and after peak calling to validate signal enrichment before downstream analysis.
Yes, it organizes output results under an all_chip_qc directory structure and supports integration with standard QC reporting workflows for downstream analysis.
The skill computes NSC, RSC, and FRiP metrics from aligned BAMs and peak files, providing the cross-correlation and enrichment values needed for ChIP-seq quality control.
This skill requires pre-aligned filtered BAMs and called peak files as input, meaning it cannot perform alignment or peak calling itself and only provides post-calling QC metrics.
BIsnake2001Automate peak calling from BAM files for ChIP-seq and ATAC-seq experiments.
zongtingweiProcess ATAC-seq data into QC metrics, peak calls, and accessible region summaries.
ya-wayAutomate ChIP-seq analysis from FASTQ to annotated peaks with MACS3 and ChIPseeker.
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