bulk-wgcna-analysis-with-omicverse
Assist Claude in running PyWGCNA through omicverse—preprocessing expression matrices, constructing co-expression modules, visualising eigengenes, and extracting hub genes.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-wgcna-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 WGCNA analysis with omicverse ## Overview 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. ## Instructions 1. **Prepare the environment** - Import `omicverse as ov`, `scanpy as sc`, `matplotlib.pyplot as plt`, and `pandas as pd`. - Set plotting defaults via `ov.plot_set()`. 2. **Load and filter expression data** - Read expression matrices (e.g., from `expressionList.csv`). - Calculate median absolute deviation with `from statsmodels import robust` and `gene_mad = data.apply(robust.mad)`. - Keep the top variable genes (e.g., `data = data.T.loc[gene_mad.sort_values(ascending=False).index[:2000]]`). 3. **Initialise PyWGCNA** - Create `pyWGCNA_5xFAD = ov.bulk.pyWGCNA(name=..., species='mus musculus', geneExp=data.T, outputPath='', save=True)`. - Confirm `pyWGCNA_5xFAD.geneExpr` looks correct before proceeding. 4. **Preprocess the dataset** - Run `pyWGCNA_5xFAD.preprocess()` to drop low-expression genes and problematic samples
- Overview
- Instructions
- Examples
- References
What does the bulk-wgcna-analysis-with-omicverse skill do?
Assist Claude in running PyWGCNA through omicverse—preprocessing expression matrices, constructing co-expression modules, visualising eigengenes, and extracting hub genes.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bulk-wgcna-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.