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bulk-rna-seq-deseq2-analysis-with-omicverse

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisWritingbulk-deseq2-analysis🔬 omics & computational biologysingle-cell & spatial omicswalk

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bulk-deseq2-analysis

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Use this skill when a user wants to reproduce the DESeq2 workflow showcased in 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.
  • 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].
  • Ensure the appropriate mapping pair exists by running ov.utils.download_geneid_annotation_pair().

Source Doc

Excerpt From SKILL.md

Examples

  • "Run PyDESeq2 on treated vs control replicates and highlight the top enriched WikiPathways terms."
  • "Filter DEGs to genes with log2(BaseMean) > 1, auto-select fold-change cutoffs, and create volcano and boxplots."
  • "Generate the ranked gene list for GSEA and plot the enrichment curve for the top pathway."

Use cases

  • Use bulk-rna-seq-deseq2-analysis-with-omicverse to prepare publication-quality figures.
  • Apply bulk-rna-seq-deseq2-analysis-with-omicverse when results need clear visual communication.

Not for

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

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