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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Full-text index only
Screening large-scale association study data: exploiting interactions using random forests.
PMID 15588316 · PMC545646 · BMC genetics · 2004 · 7 claims · 3 setups
Random forest importance measure significantly outperforms the Fisher Exact test as a screening tool when risk SNPs interact.
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Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples.
PMID 18793462 · PMC2537568 · BMC bioinformatics · 2008 · 8 claims · 4 setups
Batch size affects genotype calling results (call rate and concordance) and the resulting lists of significantly associated SNPs.
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Full-text index only
Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.
PMID 19761607 · PMC2759961 · BMC bioinformatics · 2009 · 8 claims · 5 setups
2LOmb performs an omnibus permutation test on ensembles of two-locus analyses via a four-step algorithm (two-locus analysis, permutation test, global p-value determination, progressive ensemble search)
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Has reproduction · 43
TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.
PMID 36469333 · PMC9825751 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups
TransFlow is a Snakemake- and Conda-based workflow that combines state-of-the-art tools into a single, fast, scalable pipeline for MTBC WGS-based transmission analysis.