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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bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling.
PMID 37028916 · PMC10275263 · RNA (New York, N.Y.) · 2023 · 8 claims · 4 setups
bakR uses Bayesian hierarchical modeling to share information (specifically a replicate variability vs. read count trend) across transcripts, increasing statistical power for differential kinetic analysis
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Eduomics: a Nextflow pipeline to simulate -omics data for education.
PMID 41816779 · PMC12972896 · NAR genomics and bioinformatics · 2026 · 8 claims · 4 setups
Eduomics is a Nextflow DSL2 pipeline that automates generation of validated variant-calling and RNA-seq datasets for education while abstracting away technical requirements
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Has reproduction · 58
A comparative study of techniques for differential expression analysis on RNA-Seq data.
PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups
edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.
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Has reproduction · 67
Heterogeneity and Differentiation Trajectories of Infiltrating CD8+ T Cells in Lung Adenocarcinoma.
PMID 36358600 · PMC9658355 · Cancers · 2022 · 7 claims · 8 setups
Infiltrating CD8+ T cells in LUAD can be divided into ten transcriptionally distinct subsets: eight cytotoxic (CTL) subsets, one naive-like (NTL) subset, and one exhausted (ETL) subset.