bio-atac-seq-footprinting SKILL.md skillA
bio-atac-seq-footprinting from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-atac-seq-footprinting@git:20260517.81511a7Pins git:20260517.81511a7 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/bio-atac-seq-footprinting/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260517.81511a7, committed May 17, 2026
- Size
- 7,276 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
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.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## 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 \
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-atac-seq-footprinting@sha256:33313b511a926f6fThe line at the top of this page pins the label git:20260517.81511a7, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_rcb6vyzoeesytgku)
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Versions
The registry has recorded 1 version of this file, committed on May 17, 2026.
Audit of the latest version
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- pass: No instruction to send local credentials anywhere
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Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_rcb6vyzoeesytgku GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-atac-seq-footprinting GET https://markdownregistry.com/api/v1/blob/33313b511a926f6f144e6cc5e904f78e27c1cdfd3da0d211271416a0251afa29
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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