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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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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Has reproduction · 85
Digital sorting of complex tissues for cell type-specific gene expression profiles.
PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups
The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.
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A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.
PMID 17996079 · PMC2206057 · BMC bioinformatics · 2007 · 8 claims · 7 setups
An HMM using paired germline genotype calls and tumour allelic SNP intensities can estimate allele-specific copy-numbers, distinguishing events like uniparental disomy from allelic imbalance.
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Minisequencing mitochondrial DNA pathogenic mutations.
PMID 18402672 · PMC2377236 · BMC medical genetics · 2008 · 7 claims · 7 setups
A minisequencing multiplex assay can interrogate 25 pathogenic mtDNA mutations across the whole mtDNA genome in a single reaction using 13 amplicons.