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).

• saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval.

  PMID 41709279 · PMC13019952 · Genome biology · 2026 · 8 claims · 5 setups

  Full-text index only

  Replacing the library-size offset with the log of the total gene count in NB-based bulk RNA-seq models (edgeR/DESeq2) lets the mean-model parameters be interpreted as transcript/exon usage, unlocking these tools for differential usage and aberrant splicing without DEXSeq-style subject-specific blocking covariates.

  simulated bulk cohort aberrant differential exon

• SpliceHarmonization: an integrated method for identifying RNA splicing events in therapeutics for splicing modulation.

  PMID 41858229 · PMC13064980 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups

  Full-text index only

  SpliceHarmonization integrates rMATS, LeafCutter, and MAJIQ outputs into a unified junction-centered format with standardized event type annotations via event graph construction

  sma simulated bulk splicing rt-pcr

• Functional analysis of novel SNPs and mutations in human and mouse genomes.

  PMID 19091009 · PMC2638150 · BMC bioinformatics · 2008 · 8 claims · 7 setups

  Full-text index only

  FANS streamlines functional analysis of novel SNPs and mutations into a simplified, few-click, four-step procedure.

  apoe 11-nucleotide sequence genomic manual automated exonic

• Improved reconstruction of transcripts and coding sequences from RNA-seq data.

  PMID 41700087 · PMC12910111 · Nucleic acids research · 2026 · 7 claims · 3 setups

  Full-text index only

  GeMoSeq combines combinatorial enumeration of candidate transcripts, splitting heuristics, and likelihood-based (EM) quantification for transcript reconstruction from RNA-seq data

  arabidopsis nicotiana mapped rna-seq-based combined read

• Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.

  PMID 35869080 · PMC9307511 · Nature communications · 2022 · 7 claims · 4 setups

  Has reproduction · 80

  DiffScan is a computational framework combining a Normalization module and a Scan module to identify SVRs at nucleotide resolution from SP data.

  transcripts platforms bacillus multi-subcellular simulated negative benchmark