bio-atac-seq-footprinting skillA
bio-atac-seq-footprinting is agent-read markdown (skill) from pku-yuangroup/openai4s: Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions..
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What the file says
## Version Compatibility Reference examples tested with: TOBIAS 0.16+, RGT HINT-ATAC 1.0.2+, Wellington (pyDNase) 0.3+, scprinter 0.1+, samtools 1.19+, bedtools 2.31+, pyBigWig 0.3+, MEME suite 5.5+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws unexpected errors, introspect the installed package and adapt rather than retrying. # TF Footprinting **"Identify TF binding footprints in my ATAC-seq data"** -> Detect short DNA stretches (typically 6-20 bp) of reduced Tn5 cleavage within accessible regions, where a bound TF physically protects DNA. Requires (1) Tn5 sequence-bias correction, (2) per-base footprint scoring, (3) motif-anchored detection. - CLI: `TOBIAS ATACorrect` -> `TOBIAS ScoreBigwig` (formerly `FootprintScores`) -> `TOBIAS BINDetect` - CLI: `rgt-hint footprinting --atac-seq` (HINT-ATAC, single-step) - CLI: `wellington_footprints.py` (legacy DNase, adapted for ATAC) - Python: `scprinter` (multi-scale, single-cell aware; Hu 2025 Nature) …
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How to install
mdr add pku-yuangroup/openai4s/bio-atac-seq-footprinting@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-atac-seq-footprinting@sha256:5fe6ced0856d7d79Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_vzgaen5n6yrkvheg GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-atac-seq-footprinting GET https://markdownregistry.com/api/v1/blob/5fe6ced0856d7d794c3ee91084e594ec0704d9cb9c013be37488bfce2e898987
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