bulk-rna-seq-differential-expression-with-omicverse
Guide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping and DESeq2 normalization to statistical testing, visualization, and pathway enrichment. Use when a user has bulk count matrices and needs differential expression analysis in omicverse.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-deg-analysis --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Bulk RNA-seq differential expression with omicverse ## Overview Follow this skill to run the end-to-end differential expression (DEG) workflow showcased in [`t_deg.ipynb`](../../omicverse_guide/docs/Tutorials-bulk/t_deg.ipynb). It assumes the user provides a raw gene-level count matrix (e.g., from featureCounts) and wants to analyse bulk RNA-seq cohorts inside omicverse. ## Instructions 1. **Set up the session** - Import `omicverse as ov`, `scanpy as sc`, and `matplotlib.pyplot as plt`. - Call `ov.plot_set()` so downstream plots adopt omicverse styling. 2. **Prepare ID mapping assets** - When gene IDs must be converted to gene symbols, instruct the user to download mapping pairs via `ov.utils.download_geneid_annotation_pair()` and store them under `genesets/`. - Mention the available prebuilt genomes (T2T-CHM13, GRCh38, GRCh37, GRCm39, danRer7, danRer11) and that users can generate their own mapping from GTF files if needed. 3. **Load the raw counts** - Read tab-delimited featureCounts output with `ov.pd.read_csv(..., sep='\t', header=1, index_col=0)`. - Strip trailing `.bam` segments from column names using list comprehension so sample IDs are clean. 4. **Map gene identifiers**
- Overview
- Instructions
- Examples
- References
What does the bulk-rna-seq-differential-expression-with-omicverse skill do?
Guide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping and DESeq2 normalization to statistical testing, visualization, and pathway enrichment. Use when a user has bulk count matrices and needs differential expression analysis in omicverse.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-deg-analysis --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.