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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SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes.
PMID 16845091 · PMC1538889 · Nucleic acids research · 2006 · 8 claims · 4 setups
SNPmasker is a web service combining SNP masking and repeat masking, supporting both coordinate-defined and homology-search-defined input regions, a combination not offered by prior tools
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The use of edge-betweenness clustering to investigate biological function in protein interaction networks.
PMID 15740614 · PMC555937 · BMC bioinformatics · 2005 · 8 claims · 7 setups
Edge-Betweenness clustering separates protein interaction graphs into subgraphs whose GO term distributions show significant correlations, revealing biologically meaningful functional modules.
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Has reproduction · 79
RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data.
PMID 36339261 · PMC9626663 · iScience · 2022 · 8 claims · 4 setups
RetroSnake is an end-to-end, modular, computationally efficient Snakemake pipeline for detecting HERV-K insertions in short-read NGS data, from raw alignment files to an annotated interactive HTML report
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A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts.
PMID 15626332 · PMC5172250 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 6 setups
Repeats of different copy number have distinct probabilities of appearance in shotgun data, which can be modeled statistically to define recognition thresholds (MDRs) at different shotgun coverages.