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 · 79
RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data.
PMID 36339261 · PMC9626663 · iScience · 2022 · 8 claims · 4 setups
RetroSnake is an end-to-end, modular, computationally efficient Snakemake pipeline for detecting HERV-K insertions in short-read NGS data, from raw alignment files to an annotated interactive HTML report
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Has reproduction · 58
A comparative study of techniques for differential expression analysis on RNA-Seq data.
PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups
edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.
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Full-text index only
GENCODE: producing a reference annotation for ENCODE.
PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups
GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions
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Has reproduction · 86
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.
PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups
RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.