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).

• Cancer genome standards for long-read sequencing using cancer cell line mixtures.

  PMID 41934171 · PMC13137868 · GigaScience · 2026 · 8 claims · 6 setups

  Full-text index only

  Long-read variant calling tools achieve recall rates comparable to short-read gold standards

  colo829 same whole-genome short-read 5mc

• DoBSeqWF: a framework for sensitive detection of individual genetic variation in pooled sequencing data.

  PMID 41704565 · PMC12907731 · NAR genomics and bioinformatics · 2026 · 7 claims · 5 setups

  Full-text index only

  DoBSeqWF, a Nextflow-based pipeline, processes pooled DoBSeq sequencing data through alignment, variant calling, machine-learning-based filtering, and variant pinpointing/assignment to individuals.

  individual pooled individuals gatk-called whole-genome overlapped simulated

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.

  PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 7 claims · 6 setups

  Has reproduction · 50

  MEDUSA correctly identifies more species than MEGAN 6 CE, especially less abundant species.

  bovine simulated cami datasets read host-sequence metagenome