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 · 82
Landscape of allele-specific transcription factor binding in the human genome.
PMID 33980847 · PMC8115691 · Nature communications · 2021 · 8 claims · 6 setups
A novel statistical framework (ADASTRA) calls allele-specific TF binding from existing ChIP-Seq alignments by jointly correcting for background allelic dosage (BAD, from aneuploidy/CNVs) and reference mapping bias.
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Has reproduction · 87
Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads.
PMID 38940130 · PMC11256924 · Bioinformatics (Oxford, England) · 2024 · 7 claims · 5 setups
Forseti is the first probabilistic model for resolving the splicing status of exonic scRNA-seq reads by scoring putative fragments linking read alignments to proximate priming sites
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Has reproduction · 63
Community assessment of methods to deconvolve cellular composition from bulk gene expression.
PMID 39191725 · PMC11350143 · Nature communications · 2024 · 8 claims · 4 setups
Most deconvolution methods accurately predict coarse-grained immune/stromal cell populations from bulk expression.
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omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.
PMID 41582216 · PMC12837286 · Genome biology · 2026 · 8 claims · 6 setups
omnideconv is an R package providing a unified interface to twelve second-generation deconvolution methods (AutoGeneS, BayesPrism, Bseq-SC, Bisque, CDseq, CIBERSORTx, CPM, DWLS, MOMF, MuSiC, SCDC, Scaden)