bio-chipseq-differential-binding
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values. Use when comparing ChIP-seq binding between conditions.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-differential-binding --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: DESeq2 1.42+, edgeR 4.0+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Differential Binding with DiffBind **"Compare ChIP-seq binding between conditions"** → Identify genomic regions with statistically significant differences in transcription factor or histone mark occupancy between experimental groups. - R: `DiffBind::dba()` → `dba.count()` → `dba.contrast()` → `dba.analyze()` ## Create Sample Sheet **Goal:** Define the experimental design linking BAM files, peak files, and sample metadata for DiffBind. **Approach:** Build a data frame (or CSV) with required columns mapping each sample to its files and conditions. ```r # Create sample sheet as data frame or CSV samples <- data.frame( SampleID = c('ctrl_1', 'ctrl_2', 'treat_1', 'treat_2'), Tissue = c('cell', 'cell', 'cell', 'cell'), Factor = c('H3K4me3', 'H3K4me3', 'H3K4me3', 'H3K4me3'), Condition = c('control'
- Version Compatibility
- Create Sample Sheet
- Load Data
- Count Reads in Peaks
- Normalize Data
- Set Up Contrast
- Run Differential Analysis
- View Results
- Filter Results
- Export Results
- Visualization
- Venn Diagram of Peaks
- Profile Plots
- Get Consensus Peaks
What does the bio-chipseq-differential-binding skill do?
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values. Use when comparing ChIP-seq binding between conditions.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-chipseq-differential-binding --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.