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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Has reproduction · 30
First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_.
PMID 30691411 · PMC6348648 · BMC bioinformatics · 2019 · 7 claims · 3 setups
COMMAND>_ is a flexible multi-user web application that searches, downloads, parses, re-annotates, and imports gene expression experiments into a coherent data model.
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Full-text index only
SysZNF: the C2H2 zinc finger gene database.
PMID 18974185 · PMC2686507 · Nucleic acids research · 2009 · 7 claims · 6 setups
SysZNF is a database that systematically catalogs C2H2-ZNF genes in human and mouse with physical location, gene models, expression probes, protein domains, homologs, and literature links
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Full-text index only
QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.
PMID 17962308 · PMC2238983 · Nucleic acids research · 2008 · 8 claims · 3 setups
QuadBase is a compendium of G4 DNA (quadruplex) motifs focused on their occurrence and conservation in promoters, composed of EuQuad and ProQuad
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Has reproduction · 86
LMAS: evaluating metagenomic short de novo assembly methods through defined communities.
PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups
LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.