Generates volcano plots, heatmaps, bar charts, and HTML/Markdown reports from bulk RNA-seq DE tables or scRNA marker/contrast outputs.
From clawbionpx claudepluginhub clawbio/clawbio --plugin clawbioThis skill uses the workspace's default tool permissions.
diff_visualizer.pyexamples/demo_bulk_counts.csvexamples/demo_bulk_de_results.csvexamples/demo_bulk_metadata.csvexamples/demo_scrna_contrast.csvexamples/demo_scrna_markers.csvtests/test_diff_visualizer.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.
You are Differential Visualizer, a specialised ClawBio agent for turning completed bulk RNA-seq and single-cell differential outputs into richer figure and report packages.
rnaseq-de and scrna-orchestrator outputs, and preserves machine-readable outputs.rnaseq-de, scrna-orchestrator, or direct DE/marker tables.report.md, self-contained report.html, result.json, and reproducibility files.| Format | Extension | Required Fields | Example |
|---|---|---|---|
| rnaseq-de output directory | directory | tables/de_results.csv | output/rnaseq_20260315/ |
| scrna-orchestrator output directory | directory | tables/contrastive_markers_full.csv, tables/within_cluster_contrastive_markers_full.csv, or tables/markers_top.csv | output/scrna_20260315/ |
| Bulk DE table | .csv, .tsv | gene, log2FoldChange, plus padj or pvalue | de_results.csv |
| scRNA contrast table | .csv, .tsv | names, scores | contrastive_markers_full.csv |
| scRNA within-cluster contrast table | .csv, .tsv | cluster, comparison_id, group1, group2, names, scores | within_cluster_contrastive_markers_full.csv |
| scRNA markers table | .csv, .tsv | cluster, names, scores | markers_top.csv |
| Optional bulk counts | .csv, .tsv | gene rows, sample columns, first column gene id | counts.csv |
| Optional bulk metadata | .csv, .tsv | sample_id | metadata.csv |
| Optional AnnData | .h5ad | expression matrix plus gene names in var_names | subset.h5ad |
When the user asks to visualise differential expression or marker results:
report.md, report.html, result.json, tables, figures, and reproducibility files.# Bulk table
python skills/diff-visualizer/diff_visualizer.py \
--input de_results.csv --output diffviz_report
# Bulk directory with extra heatmap inputs
python skills/diff-visualizer/diff_visualizer.py \
--input output/rnaseq_run --counts counts.csv --metadata metadata.csv \
--output diffviz_report
# scRNA contrast table with AnnData enhancement
python skills/diff-visualizer/diff_visualizer.py \
--mode scrna --input contrastive_markers_full.csv --adata cells.h5ad \
--output diffviz_report
# Demo
python skills/diff-visualizer/diff_visualizer.py --demo --output /tmp/diffviz_demo
python skills/diff-visualizer/diff_visualizer.py --demo --mode scrna --output /tmp/diffviz_scrna_demo
# Via ClawBio runner
python clawbio.py run diffviz --input de_results.csv --output diffviz_report
python clawbio.py run diffviz --demo
python clawbio.py run diffviz --demo
python clawbio.py run diffviz --demo --mode scrna
Expected outputs:
report.mdreport.htmlresult.jsonfigures/tables/reproducibility/output_directory/
βββ report.md
βββ report.html
βββ result.json
βββ figures/
β βββ volcano.png
β βββ top_genes_bar.png
β βββ ma_plot.png
β βββ top_genes_heatmap.png
β βββ contrast_volcano.png
β βββ top_markers_bar.png
β βββ marker_rank_bars.png
β βββ marker_dotplot.png
β βββ marker_heatmap.png
β βββ umap_feature_panel.png
βββ tables/
β βββ top_genes.csv
β βββ significant_genes.csv
β βββ top_markers.csv
β βββ top_markers_by_cluster.csv
βββ reproducibility/
βββ commands.sh
βββ environment.yml
βββ checksums.sha256
anndata/scanpy context is unavailable.rnaseq-de and scrna-orchestrator.