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Data & ReproSingle-Cell & Spatial OmicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction
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bulk-wgcna-analysis-with-omicverse

Maintainer FreedomIntelligence · Last updated April 1, 2026

Activate this skill for users who want to reproduce the WGCNA workflow from [`t_wgcna.ipynb`](../../omicverse_guide/docs/Tutorials-bulk/t_wgcna.ipynb). It guides you through loading expression data, configuring PyWGCNA, constructing weighted gene co-expression networks, and inspecting modules of interest.

OpenClawNanoClawAnalysisReproductionbulk-wgcna-analysis🔬 omics & computational biologysingle-cell & spatial omicsassist

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Activate this skill for users who want to reproduce the WGCNA workflow from t_wgcna.ipynb. It guides you through loading expression data, configuring PyWGCNA, constructing weighted gene co-expression networks, and inspecting modules of interest.
  • Import omicverse as ov, scanpy as sc, matplotlib.pyplot as plt, and pandas as pd.
  • Set plotting defaults via ov.plot_set().
  • Read expression matrices (e.g., from expressionList.csv).
  • Calculate median absolute deviation with from statsmodels import robust and gene_mad = data.apply(robust.mad).

Source Doc

Excerpt From SKILL.md

Examples

  • "Build a WGCNA network on the 5xFAD dataset, visualise modules, and extract hub genes from the lightgreen module."
  • "Load sample metadata, update colours for sex and genotype, and plot module eigengene heatmaps."
  • "Create a sub-network plot for the gold module using a correlation threshold of 0.2."

Use cases

  • Use bulk-wgcna-analysis-with-omicverse for single-cell or spatial omics analysis.
  • Apply bulk-wgcna-analysis-with-omicverse to clustering, integration, or trajectory workflows.

Not for

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

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