bio-splicing-quantification skillA
bio-splicing-quantification is agent-read markdown (skill) from pku-yuangroup/openai4s: Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE),.
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What the file says
## Version Compatibility
Reference examples tested with: rMATS-turbo 4.3+, SUPPA2 2.4+, leafcutter 0.2.9+, MAJIQ 3.0+, IRFinder-S 2.0+, kallisto 0.50+, Salmon 1.10+, pandas 2.2+, STAR 2.7.11+
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# Splicing Quantification
Quantify alternative splicing events as PSI (percent spliced in) from RNA-seq. PSI = inclusion read evidence / (inclusion + skipping read evidence), normalized for differential mapping opportunity between isoforms. The choice of *quantification unit* (event, intron cluster, LSV, transcript) determines which biological questions can be answered and which failure modes apply.
## Algorithmic Taxonomy
| Family | Unit | Reference tools | Fails when |
|--------|------|-----------------|------------|
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How to install
mdr add pku-yuangroup/openai4s/bio-splicing-quantification@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-splicing-quantification@sha256:a72e3ca296970c57Pin 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
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