bio-atac-seq-motif-deviation
Analyze transcription factor motif accessibility variability using chromVAR. Use when identifying which TF motifs show variable accessibility across samples or conditions in ATAC-seq data.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-motif-deviation --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: ggplot2 3.5+, limma 3.58+ 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. # Motif Deviation Analysis **"Which TF motifs show variable accessibility across my samples?"** → Compute per-sample deviation scores for TF motif accessibility to identify regulators driving chromatin state differences. - R: `chromVAR::computeDeviations(counts, motifs)` Measure per-sample variability in transcription factor motif accessibility using chromVAR. This identifies TFs whose binding sites show differential accessibility across conditions. ## Required Packages ```r library(chromVAR) library(motifmatchr) library(BSgenome.Hsapiens.UCSC.hg38) # or appropriate genome library(JASPAR2020) library(TFBSTools) library(SummarizedExperiment) ``` ## Basic Workflow **Goal:** Run chromVAR to compute per-sample TF motif deviation scores from ATAC-seq peak counts. **Approach:** Load peak counts int
- Version Compatibility
- Required Packages
- Basic Workflow
- 1. Load Peak Counts
- 2. Add GC Bias Correction
- 3. Filter Low-Quality Peaks
- Get Motif Annotations
- From JASPAR
- From CIS-BP or Custom PWMs
- Compute Deviations
- Interpreting Results
- Deviation Scores
- Variability Interpretation
- Visualization
What does the bio-atac-seq-motif-deviation skill do?
Analyze transcription factor motif accessibility variability using chromVAR. Use when identifying which TF motifs show variable accessibility across samples or conditions in ATAC-seq data.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-motif-deviation --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.