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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Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.
PMID 17663790 · PMC2323240 · Genome biology · 2007 · 8 claims · 6 setups
A sheep BAC library (CHORI-243) with ~13.5-fold genome coverage was constructed and end-sequenced.
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Frag'n'Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments.
PMID 41486154 · PMC12828970 · BMC bioinformatics · 2026 · 8 claims · 8 setups
Frag'n'Flow is a Nextflow-based pipeline that encapsulates FragPipe, automating manifest/workflow generation, tool dependency management, and downstream analysis for HPC/cloud/cluster environments.
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Has reproduction · 80
VGEA: an RNA viral assembly toolkit.
PMID 34567846 · PMC8428259 · PeerJ · 2021 · 8 claims · 5 setups
VGEA is a Snakemake workflow that chains existing tools (fastp, BWA, SAMtools, IVA, shiver, SeqKit, QUAST, MultiQC) into an all-in-one RNA viral genome assembly pipeline
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Has reproduction · 88
Wochenende - modular and flexible alignment-based shotgun metagenome analysis.
PMID 36368923 · PMC9650795 · BMC genomics · 2022 · 8 claims · 6 setups
Wochenende is a modular, transparent alignment-based pipeline for shotgun metagenome analysis supporting short and long reads across all kingdoms of life
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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)