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 · 62
E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data.
PMID 40716058 · PMC12318280 · STAR protocols · 2025 · 6 claims · 3 setups
E3RC is a computational framework for identifying and quantifying eRNAs and characterizing their expression and transcriptional regulation using conventional RNA-seq data.
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Full-text index only
Eukan: a fully automated nuclear genome annotation pipeline for less studied and divergent eukaryotes.
PMID 41567515 · PMC12817076 · NAR genomics and bioinformatics · 2026 · 8 claims · 7 setups
Eukan automatically leverages RNA-Seq coverage to inform generalized Hidden Markov Model gene prediction and intron lengths to inform protein sequence alignments
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Has reproduction · 67
A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.
PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups
Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.
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Has reproduction · 94
BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.
PMID 35704392 · PMC9546494 · The Plant journal : for cell and molecular biology · 2022 · 8 claims · 6 setups
BaRTv2.18 is the most comprehensive and resolved reference transcriptome in barley to date, containing 39,434 genes and 148,260 transcripts