bulk-rna-seq-deseq2-analysis-with-omicverse
Walk Claude through PyDESeq2-based differential expression, including ID mapping, DE testing, fold-change thresholding, and enrichment visualisation.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-deseq2-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 DESeq2 analysis with omicverse ## Overview Use this skill when a user wants to reproduce the DESeq2 workflow showcased in [`t_deseq2.ipynb`](../../omicverse_guide/docs/Tutorials-bulk/t_deseq2.ipynb). It covers loading raw featureCounts matrices, mapping Ensembl IDs to symbols, running PyDESeq2 via `ov.bulk.pyDEG`, and exploring downstream enrichment plots. ## Instructions 1. **Import and format the expression matrix** - Call `import omicverse as ov` and `ov.utils.ov_plot_set()` to standardise visuals. - Read tab-separated count data from featureCounts using `ov.utils.read(..., index_col=0, header=1)`. - Strip trailing `.bam` from column names with `[c.split('/')[-1].replace('.bam', '') for c in data.columns]`. 2. **Map gene identifiers** - Ensure the appropriate mapping pair exists by running `ov.utils.download_geneid_annotation_pair()`. - Replace `gene_id` with gene symbols using `ov.bulk.Matrix_ID_mapping(data, 'genesets/pair_<GENOME>.tsv')`. 3. **Initialise the DEG object** - Create `dds = ov.bulk.pyDEG(data)` from the mapped counts. - Resolve duplicate gene names with `dds.drop_duplicates_index()` and confirm success in logs. 4. **Define contrasts and run DESeq2*
- Overview
- Instructions
- Examples
- References
What does the bulk-rna-seq-deseq2-analysis-with-omicverse skill do?
Walk Claude through PyDESeq2-based differential expression, including ID mapping, DE testing, fold-change thresholding, and enrichment visualisation.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-deseq2-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.