bio-chipseq-motif-analysis SKILL.md skillA
bio-chipseq-motif-analysis from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-chipseq-motif-analysis@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
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- SKILL.md skill
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- pku-yuangroup/openai4s
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skills/bioskills/bio-chip-seq-motif-analysis/SKILL.md- Versions recorded
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- git:20260821.2d1b678, committed Aug 21, 2026
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- MIT
Discovers de novo motifs and tests known motif enrichment in ChIP-seq, ATAC-seq, or other peak sequences using HOMER, MEME-ChIP (STREME, CentriMo, TOMTOM, FIMO), monaLisa, and AME. Handles background selection (GC-matched, dinucleotide-shuffled, Markov order-2, peak-flanks), motif databases (JASPAR 2024 CORE PWMs, JASPAR 2026 deep-learning collection, HOCOMOCO v12, HOMER built-in), centrally-enriched motif testing, and differential motif analysis. Use when identifying TF binding motifs in…
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What the file says
## Version Compatibility Reference examples tested with: HOMER 4.11+, MEME suite 5.5+ (STREME replaces DREME from 5.4+), monaLisa 1.10+, JASPAR 2024 CORE, HOCOMOCO v12, BioPython 1.83+, bedtools 2.31+. DREME was removed from MEME suite 5.4+; use STREME instead. Some tutorials still reference DREME — verify the installed version via `meme --version`. JASPAR 2026 (released late 2025) integrates 1259 BPNet ChIP models in a Deep Learning collection; the CORE collection remains the standard PWM source. # Motif Analysis on ChIP-seq Peaks **"Find enriched DNA binding motifs in my ChIP-seq peaks"** -> Discover de novo motif patterns and test for known TF motif enrichment in peak sequences, with appropriate background to control for compositional and positional biases. - CLI (HOMER, fast): `findMotifsGenome.pl peaks.bed hg38 outdir/ -size 200 -p 8` - CLI (MEME-ChIP, comprehensive): `meme-chip -db JASPAR.meme peaks.fa` - R (regression-based, selective enrichment): `monaLisa::calcBinnedMotifEnrR(seqs, bins, pwms)` - CLI (deep-learning-derived motifs): TF-MoDISco on BPNet attribution scores (see chip-deep-learning) …
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How to install
mdr add pku-yuangroup/openai4s/bio-chipseq-motif-analysis@sha256:0ae2ddaafff2222aThe line at the top of this page pins the label git:20260821.2d1b678, 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.
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The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
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