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 · 86
The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection.
PMID 37027361 · PMC10081788 · PloS one · 2023 · 7 claims · 7 setups
Obtaining an accurate species-level microbial profile using current direct-read metagenomics profiling software is still a challenging task.
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Has reproduction · 67
Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice.
PMID 36553546 · PMC9777648 · Genes · 2022 · 8 claims · 1 setups
16S rRNA gene sequencing enables taxonomic identification of bacteria/archaea via hypervariable regions without amplifying human DNA, but is limited by short-read biases (GC bias, sequencing errors) and poor species-level resolution
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Has reproduction · 60
UNMF: a unified nonnegative matrix factorization for multi-dimensional omics data.
PMID 37478378 · PMC10516365 · Briefings in bioinformatics · 2023 · 5 claims · 3 setups
UNMF is designed for tidy data format and structure, allowing it to handle a wide range of data structures and formats in a unified manner without requiring format-specific preprocessing.
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Has reproduction · 66
RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.
PMID 36159175 · PMC9492272 · NAR genomics and bioinformatics · 2022 · 8 claims · 6 setups
RiboTaxa, combining BBTools, FastQC, SortMeRNA, MetaRib, EMIRGE, VSEARCH, BBMap and QIIME 2's Sklearn classifier, was built as a pipeline for SSU rRNA-based taxonomic profiling of metagenomics data.