bio-atac-seq-footprinting
Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identifying TF occupancy patterns within accessible regions, as TF binding protects DNA from Tn5 cutting.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-footprinting --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: bedtools 2.31+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, pyBigWig 0.3+, samtools 1.19+ 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. # TF Footprinting **"Identify TF binding footprints in my ATAC-seq data"** → Detect protected DNA regions within accessible chromatin where bound transcription factors block Tn5 insertion. - CLI: `TOBIAS ATACorrect` → `TOBIAS FootprintScores` → `TOBIAS BINDetect` ## TOBIAS Workflow **Goal:** Identify transcription factor binding footprints within accessible chromatin regions. **Approach:** Correct Tn5 insertion bias, compute per-base footprint scores, then detect bound/unbound TF motif sites using the three-step TOBIAS pipeline. ```bash # 1. Correct Tn5 bias tobias ATACorrect \ --bam sampl
- Version Compatibility
- TOBIAS Workflow
- TOBIAS Differential Footprinting
- Download JASPAR Motifs
- Prepare Input Files
- HINT-ATAC Alternative
- PIQ Footprinting
- Aggregate Footprint Plots
- Python: Custom Footprint Analysis
- Scan for Motifs
- Interpret Footprint Depth
- Quality Considerations
- Differential TF Activity
- TOBIAS Output Files
tobias ATACorrect \ tobias FootprintScores \ tobias BINDetect \ Compare conditions Output includes: Download JASPAR motifs wget https://jaspar.genereg.net/download/data/2022/CORE/JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt mv JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt JASPAR_motifs.pfm Ensure BAM is sorted and indexed samtools sort -@ 8 sample.bam -o sample.sorted.bam
What does the bio-atac-seq-footprinting skill do?
Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identifying TF occupancy patterns within accessible regions, as TF binding protects DNA from Tn5 cutting.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-atac-seq-footprinting --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.