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 · 94
Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks.
PMID 35794110 · PMC9258765 · Nature communications · 2022 · 8 claims · 5 setups
Deep learning (FFNN-SS and CNN-CBLV) enables accurate and fast likelihood-free estimation of epidemiological parameters and model selection from phylogenies
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Has reproduction · 83
MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data.
PMID 36386613 · PMC9651917 · Frontiers in microbiology · 2022 · 7 claims · 4 setups
MetaGT is a pipeline that combines metatranscriptomic and metagenomic data from the same sample to assemble complete transcript sequences
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Has reproduction · 61
TEMP: a computational method for analyzing transposable element polymorphism in populations.
PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups
TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.
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Has reproduction · 89
TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.
PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups
TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency