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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Umi-pipeline-nf: a modular and scalable workflow for UMI-tagged nanopore amplicon analysis with real-time sequencing integration and GPU-acceleration.
PMID 41923360 · PMC13070649 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups
umi-pipeline-nf is a portable, fully containerized, modular Nextflow DSL2 workflow that generates single-molecule consensus sequences from UMI-tagged nanopore amplicon data and scales linearly from single samples to large cohorts.
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Has reproduction · 83
Hobbes: optimized gram-based methods for efficient read alignment.
PMID 22199254 · PMC3315303 · Nucleic acids research · 2012 · 8 claims · 4 setups
Hobbes, a gram-based short-read mapper supporting Hamming and edit distance, is faster than all other read-mapping programs tested while maintaining high mapping quality.
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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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CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data.
PMID 41734268 · PMC12987762 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups
CIRCE re-implements the Cicero co-accessibility algorithm in Python, producing near-identical results while running much faster and using far less memory