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).

• Dogme: a nextflow pipeline for reprocessing nanopore RNA and DNA modifications.

  PMID 41769815 · PMC12961274 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 2 setups

  Full-text index only

  Dogme automates basecalling (Dorado), alignment (minimap2), modification detection (modkit), and transcript quantification (LR-Kallisto) from raw ONT POD5 files in a single Nextflow workflow.

  c2c12 direct long-read

• MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets.

  PMID 32256520 · PMC7089958 · Frontiers in genetics · 2020 · 8 claims · 5 setups

  Has reproduction · 50

  MasterOfPores is a scalable, parallelizable, containerized (Docker/Singularity) NextFlow workflow for analyzing Oxford Nanopore direct RNA sequencing datasets

  cerevisiae barcoded direct polya modification