Performs differential expression analysis on bulk RNA-seq and pseudo-bulk count matrices, including QC, PCA, volcano/MA plots, and markdown reports.
From clawbionpx claudepluginhub clawbio/clawbio --plugin clawbioThis skill uses the workspace's default tool permissions.
examples/demo_counts.csvexamples/demo_metadata.csvrnaseq_de.pytests/fixtures/pseudobulk_counts.csvtests/fixtures/pseudobulk_metadata.csvtests/test_rnaseq_de.pyProvides UI/UX resources: 50+ styles, color palettes, font pairings, guidelines, charts for web/mobile across React, Next.js, Vue, Svelte, Tailwind, React Native, Flutter. Aids planning, building, reviewing interfaces.
Fetches up-to-date documentation from Context7 for libraries and frameworks like React, Next.js, Prisma. Use for setup questions, API references, and code examples.
Calculates TAM/SAM/SOM using top-down, bottom-up, and value theory methodologies for market sizing, revenue estimation, and startup validation.
This skill performs differential expression on bulk RNA-seq or pseudo-bulk count matrices.
.csv or .tsv): rows are genes, columns are samples, first column is gene identifier.csv or .tsv): one row per sample, must include sample_id~ condition or ~ batch + conditionfactor,numerator,denominator (e.g. condition,treated,control)rnaseq_de_report/
āāā report.md
āāā figures/
ā āāā pca.png
ā āāā volcano.png
ā āāā ma_plot.png
āāā tables/
ā āāā qc_summary.csv
ā āāā normalized_counts.csv
ā āāā de_results.csv
āāā reproducibility/
āāā commands.sh
āāā environment.yml
āāā checksums.sha256
python rnaseq_de.py \
--counts counts.csv \
--metadata metadata.csv \
--formula "~ batch + condition" \
--contrast "condition,treated,control" \
--output report_dir