Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• RummaGEO: Automatic mining of human and mouse gene sets from GEO.

  PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups

  Has reproduction · 63

  RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO

  genes rummageo rummageo-derived leiden bulk gene leiden

• The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.

  PMID 17784955 · PMC2375021 · Genome biology · 2007 · 8 claims · 6 setups

  Full-text index only

  Gene-gene functional similarity can be measured using kappa statistics applied to a binary gene-annotation-term matrix built from 14 annotation categories.

  genome protein-protein genes artificial kappa clustering gene

• GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

  PMID 40208796 · PMC11984350 · GigaScience · 2025 · 8 claims · 8 setups

  Has reproduction · 76

  GeneSetCart is a web-based platform that lets users assemble, augment, combine, visualize, and analyze gene sets from multiple sources in one place

  user-assembled archs4 generif-derived aggregated gene gene-gene literature