bio-atac-seq-differential-accessibility
Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2. Use when comparing chromatin accessibility between treatment groups, cell types, or developmental stages in ATAC-seq experiments.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-differential-accessibility --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+, GenomicRanges 1.54+, Subread 2.0+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scipy 1.12+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters - 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. # Differential Accessibility **"Find differentially accessible regions between my conditions"** → Identify chromatin regions with statistically significant changes in accessibility between treatment groups, cell types, or timepoints. - R: `DiffBind` or `DESeq2` on a peak-by-sample count matrix ## DiffBind Workflow **Goal:** Identify differentially accessible chromatin regions between experimental conditions. **Approach:** Load sample metadata and peak files into DiffBind, count reads in consensus peaks, normalize, define contrasts, and run differential analysis with DESeq2 back
- Version Compatibility
- DiffBind Workflow
- DiffBind with Consensus Peaks
- DiffBind Visualizations
- Using DESeq2 Directly
- Count Reads in Peaks
- Python Alternative
- Annotate Differential Peaks
- Filter Results
- Multi-factor Designs
- Related Skills
Using featureCounts
First convert peaks to SAF format
awk 'BEGIN{OFS="\t"; print "GeneID\tChr\tStart\tEnd\tStrand"}
featureCounts \What does the bio-atac-seq-differential-accessibility skill do?
Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2. Use when comparing chromatin accessibility between treatment groups, cell types, or developmental stages in ATAC-seq experiments.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-differential-accessibility --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.