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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DupyliCate: mining, classifying, and characterizing gene duplications.
PMID 42209743 · PMC13219399 · Scientific reports · 2026 · 8 claims · 8 setups
DupyliCate is a Python tool for identifying and classifying gene duplication arrays, using BUSCO-based species-specific thresholds and offering integrated expression divergence and Ka/Ks analysis.
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Has reproduction · 84
Pharokka: a fast scalable bacteriophage annotation tool.
PMID 36453861 · PMC9805569 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 5 setups
Pharokka is a one-line, fast, scalable bacteriophage annotation tool producing standards-compliant outputs, installable via a two-line bioconda command
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Has reproduction · 76
What the Phage: a scalable workflow for the identification and analysis of phage sequences.
PMID 36399058 · PMC9673492 · GigaScience · 2022 · 8 claims · 7 setups
WtP combines 11 tools (14 approaches) for phage prediction in a parallel, containerized Nextflow workflow
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Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.
PMID 41800382 · PMC12967217 · Bioinformatics advances · 2026 · 6 claims · 8 setups
Annotation tools show substantial variation in isoform detection, structural completeness, splicing classification, and handling of 5' read truncation when applied to plant dRNA-seq data.