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).
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Has reproduction · 79
TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining.
PMID 33705981 · PMC9403021 · Genomics, proteomics & bioinformatics · 2021 · 8 claims · 6 setups
TSUNAMI is a freely accessible web-based tool suite that mines gene co-expression network (GCN) modules from public (GEO, TCGA) or user-uploaded numerical omics data and performs downstream gene set enrichment analysis.
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CLEAN: CLustering Enrichment ANalysis.
PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups
The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).
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Has reproduction · 71
Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.
PMID 30993001 · PMC6459838 · NPJ systems biology and applications · 2019 · 8 claims · 7 setups
Retaining only the top ~3 most correlated edges per gene (EPG3) combined with FastUnfold clustering (termed PGCNA) produces gene co-expression modules with significantly better separation and enrichment of known biology than using all edges or other clustering methods.
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Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).
PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups
MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes