Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add PKU-YuanGroup/OpenAI4S --skill bio-alternative-splicing-isoform-switchinggit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alternative-splicing-isoform-switching)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alternative-splicing-isoform-switching"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alternative-splicing-isoform-switching/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alternative-splicing-isoform-switching"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alternative-splicing-isoform-switching.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00170 | $0.06250 |
| Opus 5 | $0.00085 | $0.03125 |
| Sonnet 5 | $0.00034 | $0.01250 |
| Haiku 4.5 | $0.00017 | $0.00625 |
Grade A, and why
bio-isoform-switching scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 13d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
This is a copy
95% identical to bio-isoform-switching — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 448 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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_nameto verify parameters - CLI:
<tool> --versionthen<tool> --helpto 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 |
|---|---|---|---|
| DGE Does the gene total change? | Sum of transcript counts | DESeq2, edgeR, limma-voom | "Gene X is upregulated 2-fold" |
| DTE Does this transcript change in absolute abundance? | Per-transcript count | swish (fishpond), DESeq2 on transcripts, sleuth | "Transcript X-201 is upregulated 2-fold" |
| DTU Do proportions of transcripts within the gene shift? | Vector of per-transcript proportions | DRIMSeq, DEXSeq, satuRn (+ stageR) | "Gene X switches from isoform 201 (50% -> 10%) to 202 (50% -> 90%)" |
DTU is statistically harder than DGE because:
- The null is compositional (proportions sum to 1; one transcript up means another down).
- Multi-stage testing is required: gene-level "any DTU" + transcript-level "which transcript" -> stageR formalizes this.
- Quantification uncertainty propagates when transcripts are similar (Salmon EM ambiguity).
DTU and event-level differential splicing answer related but distinct questions: rMATS' IncLevelDifference is essentially a 1-D projection of a DTU shift onto a single event coordinate. The pragmatic 2026 default: run both an event-level tool (rMATS or leafcutter) and a DTU pipeline; reconcile.
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 13d ago First seen · 448 lines · 170 tokens per session scan A c17e9a2d13b3
bio-isoform-switching is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 170 tokens to every session and 6,250 once invoked, about $0.0009 per session on Opus 5. A static security scan graded it A with 0 findings. It is 95% identical to bio-isoform-switching, differing in 12 lines, and is treated as a copy.
Other skills, from other repositories
boltz-structure-prediction
Boltz-1 / Boltz-2 structure prediction for proteins, complexes, and ligand-aware validation. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed binders, (3) Need open-source alternative to AF2, (4) Predicting protein-ligand complexes, (5) Using local GPU resources. For QC…
imaging-data-commons
Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.
flow-cytometry-analysis
Complete flow cytometry analysis pipeline. FCS file handling, compensation, manual/automated gating, immunophenotyping, CFSE proliferation analysis, cell cycle analysis (Dean-Jett-Fox), and apoptosis assays. Extends flowio with analytical workflows. For raw FCS parsing only use flowio.
scientific-critical-thinking
Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review…
cellxgene-census
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries, reference atlas comparisons. For analyzing your own data use scanpy or scvi-tools.
glycobiology
Glycosylation site prediction and glycobiology analysis. N-glycosylation motif finding, O-glycosylation hotspot prediction, glycan structure resources. Lightweight, pure Python. For protein function queries use uniprot-database; for structure analysis use alphafold-database.