Choosing A Path

Use this page to decide which part of the project to start with.

I Have Normalized Gene Sets And Want Enrichment

Use the Rust CLI directly:

genesets-rs matrix \
  --target-sets library.gmt \
  --target-format gmt \
  --queries samples.gmt \
  --query-format gmt \
  --output-format parquet \
  --output results.parquet

Start with Getting Started, then read the Input Model and CLI Reference.

I Need To Fetch Sources Or Run A Repeatable Report

Use genesets-workflows. The workflow layer owns downloads, source-specific filtering, GO/GOA or Reactome preparation, metadata, and report summaries:

uv run --project python/genesets-workflows genesets-workflows doctor
genesets-workflows go-impact evals/go_impact_5y_expression500.yaml

Start with Reports And Evals and Workflow Layer.

I Want To Inspect Existing Eval Results In A Browser

Use the local web explorer. It reads workflow report bundles and does not run enrichment itself:

just browser

Start with Web Explorer and Report Bundles.

I Want Curated Gene Set Interpretations

Use the curation/ corpus. Each curated YAML file records what a non-GO gene set should mean in GO terms, including curator categories, confidence, specificity, recovery status, enrichment stats, and evidence.

Start with Curated Gene Set Interpretations, then read the Curation Workflow and Schema Reference.

I Want A Public Browser For Curated Gene Sets

Build it as static pages or a workflow-layer web view over the curated YAML, not as a Rust-core feature. The recommended path is described in Static Browser Plan.