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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BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.
PMID 19668202 · PMC3661775 · Nature methods · 2009 · 8 claims · 8 setups
BreakDancer (BreakDancerMax + BreakDancerMini) is a software package that predicts a wide variety of structural variants including deletions, insertions, inversions, and intra/inter-chromosomal translocations from paired-end short-insert sequencing reads.
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Has reproduction · 69
Discovery and characterization of Alu repeat sequences via precise local read assembly.
PMID 26503250 · PMC4666360 · Nucleic acids research · 2015 · 7 claims · 8 setups
Combining Alu-supporting read detection (RetroSeq) with local de novo assembly (CAP3) reconstructs the full sequence of non-reference Alu insertions from Illumina paired-end WGS reads
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Has reproduction · 97
Determination of complete chromosomal haplotypes by bulk DNA sequencing.
PMID 33957932 · PMC8101039 · Genome biology · 2021 · 8 claims · 8 setups
A hierarchical computational strategy that first builds high-confidence local haplotype blocks from long-range/linked-read linkage and then concatenates them into whole-chromosome haplotypes using Hi-C contacts
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Searching for SNPs with cloud computing.
PMID 19930550 · PMC3091327 · Genome biology · 2009 · 8 claims · 4 setups
Crossbow combines the Bowtie short-read aligner and SOAPsnp SNP caller into a seamless, automatic Hadoop/MapReduce pipeline for whole-genome resequencing analysis