Individual skill
gsva-analysis-and-visualization
Use this skill to run GSVA or ssGSEA pathway-level differential analysis from a bulk expression matrix and a sample group file, then generate a heatmap from the saved GSVA result object. Trigger keywords: GSVA, ssGSEA, pathway enrichment, KEGG pathway analysis, MSigDB. NOT for: gene-level differential expression, single-cell analysis, methylation analysis, clinical diagnosis.
awesome-med-research-skills/Data Analysis/gsva-analysis-and-visualization/SKILL.md
Source commit 686e09dfdb45d9fa1a08664f06bb93769b3c9d91
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- Observed behavior
- Local scripts
- Last checked
- Nov 9, 2026
These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.
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Repository context
- Repository stars (not skill ratings)
- 2,042
- Repository last updated
- Sep 17, 2026
- License
- MIT
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- bioinformatics Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- ai Repository topic
- biology Repository topic
- cancer-genomics Repository topic
- data-visualization Repository topic
- differential-expression Repository topic
- genomics Repository topic
- medical Repository topic
- data Derived category
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Browse files
SKILL.mdcore · 15,555 bytesSKILL.mdcore · 15,555 bytesSKILL.mdcore · 15,555 bytesSKILL.mdcore · 15,555 bytesSKILL.mdcore · 15,555 bytesSKILL.mdcore · 15,555 bytesSKILL.mdcore · 15,555 byteseval_report_gsva-analysis-and-visualization_result.jsonasset · 16,262 bytesreferences/algorithm.mddoc · 2,577 bytesreferences/cli-guide.mddoc · 5,892 bytesreferences/troubleshooting.mddoc · 2,579 bytesscripts/cli_options.Rruns · 7,090 bytesscripts/functions.Rruns · 4,495 bytesscripts/io.Rruns · 3,510 bytesscripts/main.Rruns · 4,759 bytesscripts/plot_helpers.Rruns · 2,715 bytesscripts/recording.Rruns · 3,435 bytesscripts/run_analysis.Rruns · 2,315 bytesscripts/utils.Rruns · 2,893 bytesscripts/visualization.Rruns · 3,053 bytestests/data/expr_matrix.csvasset · 25,533,296 bytestests/data/group.csvasset · 2,778 bytestests/run_tests.Rruns · 2,191 bytes
Read excerpt
# GSVA Analysis And Visualization
## When to Use
Use this skill when the user wants one of the following:
- Pathway-level GSVA or ssGSEA analysis from a bulk expression matrix plus a sample group file
- Case-vs-control or treatment-vs-control pathway enrichment comparison using GSVA plus limma
- KEGG or MSigDB pathway analysis for bulk RNA-seq or microarray-like expression data
- Heatmap generation from an existing `data/GSVA_list.rda` result object
- A reproducible CLI-backed GSVA workflow with saved tables, an `.rda` object, and a PDF heatmap
Typical request patterns:
