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 · 65
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses.
PMID 33932985 · PMC8088074 · BMC bioinformatics · 2021 · 8 claims · 5 setups
SPEAQeasy is a portable, easy-to-install, Nextflow-powered RNA-seq processing pipeline that lowers the computational entry barrier for biologists/clinicians
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Has reproduction · 85
High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing.
PMID 40155798 · PMC11951665 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 6 setups
SNVs are imputed with high accuracy and recall across all tested WGS depths (1-4x), including in samples external to the reference panel.
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Has reproduction · 86
Assessing Bos taurus introgression in the UOA Bos indicus assembly.
PMID 34922445 · PMC8684283 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups
Aligning B. taurus samples to UOA_Brahman_1 detects up to 5 million more SNVs than aligning to ARS_UCD1.2, and aligning B. indicus samples to ARS_UCD1.2 detects 1.5 million more SNVs than aligning to UOA_Brahman_1, demonstrating reference-genome bias.
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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.