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bulk-rna-seq-differential-expression-with-omicverse

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisReproductionbulk-deg-analysis🔬 omics & computational biologysingle-cell & spatial omicsguide

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bulk-deg-analysis

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Follow this skill to run the end-to-end differential expression (DEG) workflow showcased in 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.
  • Import omicverse as ov, scanpy as sc, and matplotlib.pyplot as plt.
  • Call ov.plot_set() so downstream plots adopt omicverse styling.
  • 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.

Source Doc

Excerpt From SKILL.md

Examples

  • "I have a featureCounts matrix for mouse tumour samples—normalize it with DESeq2, run t-test DEG, and highlight the top 8 genes in a volcano plot."
  • "Use omicverse to compute edgeR-style differential expression between treated and control replicates, then run GO enrichment on significant genes."
  • "Guide me through converting Ensembl IDs to symbols, performing limma DEG, and plotting boxplots for Krtap9-5 and Lef1."

Use cases

  • Use when a user has bulk count matrices and needs differential expression analysis in omicverse.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

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