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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A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.
PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups
Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)
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A statistical approach for array CGH data analysis.
PMID 15705208 · PMC549559 · BMC bioinformatics · 2005 · 8 claims · 4 setups
Existing model-selection criteria (AIC, BIC, and prior ad hoc penalties) are not well adapted to estimating the number of segments in array CGH data
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ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data.
PMID 17710137 · PMC1940324 · PloS one · 2007 · 8 claims · 4 setups
ADaCGH implements eight CNA detection methods, including the best-performing ones from recent reviews (CBS, GLAD, CGHseg, HMM)
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Visualization of shared genomic regions and meiotic recombination in high-density SNP data.
PMID 19696932 · PMC2725774 · PloS one · 2009 · 8 claims · 7 setups
SNPduo is a command-line (SNPduo++) and web-accessible tool that analyzes and visualizes relatedness between two individuals using identity by state (IBS) from SNP genotypes.