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 · 67
snpQT: flexible, reproducible, and comprehensive quality control and imputation of genomic data.
PMID 34900230 · PMC8637247 · F1000Research · 2021 · 8 claims · 4 setups
snpQT is a scalable, stand-alone software pipeline using nextflow and BioContainers for comprehensive, reproducible, interactive QC of human genomic data.
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Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.
PMID 18831757 · PMC2572624 · BMC bioinformatics · 2008 · 6 claims · 4 setups
A dye intensity bias between the two channels (X/Y, Cy5/Cy3) of the Infinium II assay remains after BeadStudio's proprietary normalization.
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SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.
PMID 17971856 · PMC2034603 · PloS one · 2007 · 8 claims · 3 setups
SiDCoN is a spreadsheet-based application that simulates Ballele and logR plots for all known types of DNA copy number change, with or without stromal contamination, for up to 5000 SNP data points and up to 3 combined aberrations
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Statistical challenges in preprocessing in microarray experiments in cancer.
PMID 18829474 · PMC3529914 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 7 setups
Choice of pre-processing method materially changes which features are found significantly associated with survival in the Beer et al. lung cancer microarray dataset