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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pmid-42057295
PMID 42057295 · PMC13141149 · 8 claims · 5 setups
nf-core/viralmetagenome is a Nextflow pipeline that automates untargeted reconstruction and variant analysis of eukaryotic DNA and RNA viruses from short-read metagenomic or hybridisation-capture data.
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Optimal step length EM algorithm (OSLEM) for the estimation of haplotype frequency and its application in lipoprotein lipase genotyping.
PMID 12529185 · PMC149347 · BMC bioinformatics · 2003 · 5 claims · 4 setups
OSLEM (Optimal Step Length EM), which approximates an optimal step length via a fixed-point search (D_N = D_{N-1} + λ(D_preN - D_{N-1})), runs about twice as fast as standard EM while producing the same haplotype frequency estimates.
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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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Alpseq: an open-source workflow to turbocharge nanobody discovery with high-throughput sequencing.
PMID 41631412 · PMC12885427 · mAbs · 2026 · 8 claims · 8 setups
alpseq is an open-source, end-to-end workflow combining a PCR-free sequencing library prep protocol with a Nextflow pre-processing pipeline and an R-based analysis/reporting module for nanobody NGS data.