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 · 53
spliceJAC: transition genes and state-specific gene regulation from single-cell transcriptome data.
PMID 36321549 · PMC9627675 · Molecular systems biology · 2022 · 8 claims · 8 setups
spliceJAC uses unspliced and spliced mRNA count matrices to construct cell state-specific gene-gene regulatory interaction (Jacobian) matrices from scRNA-seq data
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Has reproduction · 40
DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data.
PMID 38950178 · PMC11236288 · Bioinformatics (Oxford, England) · 2024 · 8 claims · 2 setups
DeepGSEA is an explainable deep gene set enrichment analysis method built on interpretable, prototype-based neural networks.
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Has reproduction · 73
treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses.
PMID 34001188 · PMC8127214 · Genome biology · 2021 · 7 claims · 6 setups
treeclimbR proposes multiple candidate resolutions on a tree and selects the optimal one in a data-driven manner using three criteria (FDR-controlling range of t, number of rejected leaves, fewest internal nodes)
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Has reproduction · 50
Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data.
PMID 33746712 · PMC7966716 · Frontiers in molecular neuroscience · 2021 · 7 claims · 7 setups
sctRNA-seq datasets (particularly LCM-seq) show measurable off-target mRNA contamination from surrounding cell types