bio-isoform-switching skillA
bio-isoform-switching is agent-read markdown (skill) from pku-yuangroup/openai4s: Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annota.
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: IsoformSwitchAnalyzeR 2.11+, DRIMSeq 1.34+, DEXSeq 1.52+, satuRn 1.14+, stageR 1.28+, fishpond 2.14+, tximport 1.34+, tximeta 1.24+, Salmon 1.10+
Before using code patterns, verify installed versions match. If versions differ:
- 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.
# Isoform Switching and Differential Transcript Usage
Identify shifts in *which* transcript a gene predominantly uses between conditions, and predict functional consequences. Statistically distinct from DGE and DTE; biologically distinct because the same gene-level expression can hide a complete isoform switch with major protein-level consequences.
## DGE vs DTE vs DTU: Which Question Is Being Asked?
| Question | Statistic | Tool | Example claim |
|----------|-----------|------|----------------|
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How to install
mdr add pku-yuangroup/openai4s/bio-isoform-switching@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-isoform-switching@sha256:c17e9a2d13b32c21Pin 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_ypljca4dxc4kxyyj)
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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_ypljca4dxc4kxyyj GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-isoform-switching GET https://markdownregistry.com/api/v1/blob/c17e9a2d13b32c21de28120c95619ee5482d58e522f24e56758e3a60193d1da4
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