bio-chipseq-peak-calling
ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports input control, fragment size modeling, and various output formats including narrowPeak and broadPeak BED files. Use when calling peaks from ChIP-seq alignments.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-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.
## Version Compatibility Reference examples tested with: MACS2 2.2+, MACS3 3.0+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Peak Calling with MACS3 **"Call peaks from my ChIP-seq data"** → Identify significantly enriched regions (narrow peaks for TFs, broad peaks for histone marks) by comparing IP signal to input control. - CLI: `macs3 callpeak -t chip.bam -c input.bam -f BAM -g hs -n sample` MACS3 is the actively developed successor to MACS2. Commands are identical except the binary name. MACS2 is in maintenance mode. ## Basic Peak Calling **Goal:** Call enriched regions from ChIP-seq alignments with input control normalization. **Approach:** Compare treatment BAM signal against input control using MACS3 local Poisson model. ```bash # Call peaks with input control (recommended) macs3 callpeak -t chip.bam -c input.bam -f BAM -g hs -n sample --outdir peaks/ # For MACS2 (legacy), replace 'macs3' with 'macs2' - syntax is identi
- Version Compatibility
- Basic Peak Calling
- Without Input Control
- Narrow Peaks (TF, H3K4me3, H3K27ac)
- Broad Peaks (H3K36me3, H3K27me3, H3K9me3)
- Paired-End Data
- Multiple Replicates
- Custom Genome Size
- Common Genome Sizes
- Fixed Fragment Size
- Generate Signal Tracks
- Local Lambda for Broad Marks
- Cutoff Analysis
- Output Files
Call peaks with input control (recommended) macs3 callpeak -t chip.bam -c input.bam -f BAM -g hs -n sample --outdir peaks/ For MACS2 (legacy), replace 'macs3' with 'macs2' - syntax is identical Not recommended, but possible macs3 callpeak -t chip.bam -f BAM -g hs -n sample --outdir peaks/ macs3 callpeak \ MACS3 uses BAMPE format for paired-end Pool replicates (MACS3 handles internally) For non-model organisms or custom genomes If modeling fails or for ATAC-seq
What does the bio-chipseq-peak-calling skill do?
ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports input control, fragment size modeling, and various output formats including narrowPeak and broadPeak BED files. Use when calling peaks from ChIP-seq alignments.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.