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 · 67
SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes.
PMID 36875992 · PMC9978240 · F1000Research · 2022 · 7 claims · 8 setups
SnakeMAGs is a simple, efficient, flexible and scalable Snakemake workflow that processes Illumina reads from raw data to MAG classification and relative abundance estimation
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Full-text index only
Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.
PMID 18788775 · PMC3744223 · Journal of proteome research · 2008 · 7 claims · 4 setups
PeptideProphet's fixed LDA coefficients for combining search scores (Xcorr', ΔCn, SpRank) may not be optimal under all search/instrument conditions.
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Has reproduction · 100
nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.
PMID 35118380 · PMC8808542 · NAR genomics and bioinformatics · 2022 · 8 claims · 7 setups
nf-core/mag is a Nextflow/nf-core pipeline for hybrid metagenome assembly, binning and taxonomic classification of MAGs.
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Has reproduction · 78
4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans.
PMID 33301041 · PMC7708080 · Nucleic acids research · 2020 · 7 claims · 8 setups
A 4mC orphan MTase (lomA) is present only in the pathogenic (P) clade of Leptospira and methylates CTAG motifs.