bio-atac-seq-atac-qc skillA
bio-atac-seq-atac-qc is agent-read markdown (skill) from pku-yuangroup/openai4s: ATAC-seq library quality control -- TSS enrichment, FRiP, fragment-size periodicity, library complexity (NRF/PBC1/PBC2), mitochondrial fraction, and ENCODE 4 thresholds. Use when assessing whether an ATAC-seq library passes ENCODE acceptance criteria, diagnosing transposition artefacts, comparing Omni-ATAC vs standard prep quality, or selecting which replicates to drop before peak calling..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
## Version Compatibility
Reference examples tested with: deepTools 3.5+, Picard 3.1+, samtools 1.19+, bedtools 2.31+, ATACseqQC 1.26+, pysam 0.22+, pyBigWig 0.3+, numpy 1.26+, pandas 2.2+, MultiQC 1.21+.
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.
# ATAC-seq Quality Control
**"Does my ATAC library pass ENCODE quality criteria?"** -> Compute the seven canonical metrics (depth, alignment rate, mitochondrial fraction, library complexity, fragment-size periodicity, TSS enrichment, FRiP) and compare against ENCODE 4 thresholds, then diagnose failures.
- CLI: `picard CollectInsertSizeMetrics`, `samtools flagstat`, `samtools idxstats`
- CLI: `deeptools plotFingerprint`, `computeMatrix reference-point` + `plotProfile`
- R: `ATACseqQC::TSSEscore`, `ATACseqQC::fragSizeDist`, `ATACseqQC::PTscore`
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-atac-seq-atac-qc@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-atac-seq-atac-qc@sha256:9ed115486c9165e4Pin 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.
[](https://markdownregistry.com/a/art_rwbnt23tm7sczcno)
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Versions
Audit of the latest version
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- pass: No curl or wget piped into a shell
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- pass: No base64 blob over 200 characters
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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_rwbnt23tm7sczcno GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-atac-seq-atac-qc GET https://markdownregistry.com/api/v1/blob/9ed115486c9165e423118c1abf4097f4d6eb01b5d0e8c91e5e88736b55c3ae35
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