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).

• A workflow reproducibility scale for automatic validation of biological interpretation results.

  PMID 37150537 · PMC10164546 · GigaScience · 2022 · 8 claims · 4 setups

  Has reproduction · 100

  Comparing output files by checksum alone is insufficient to verify reproducibility, since checksums can differ even when the underlying biological interpretation is unchanged

  nf-core sam vcf workflow checksum biological workflow

• GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure.

  PMID 35501696 · PMC9063052 · BMC bioinformatics · 2022 · 6 claims · 3 setups

  Has reproduction · 67

  GEMmaker, an nf-core compliant Nextflow workflow, can quantify gene expression from small to massive RNA-seq datasets while remaining reproducible via versioned containerized software.

  oryza arabidopsis generic rna-seq workflow

• pyrpipe: a Python package for RNA-Seq workflows.

  PMID 34085037 · PMC8168212 · NAR genomics and bioinformatics · 2021 · 8 claims · 3 setups

  Has reproduction · 79

  pyrpipe enables development of flexible, reproducible, and easy-to-debug RNA-Seq computational pipelines purely in Python, in an object-oriented manner

  circulating zea bulk novo

• First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_.

  PMID 30691411 · PMC6348648 · BMC bioinformatics · 2019 · 7 claims · 3 setups

  Has reproduction · 30

  COMMAND>_ is a flexible multi-user web application that searches, downloads, parses, re-annotates, and imports gene expression experiments into a coherent data model.

  small user-defined microarray affymetrix rna-seq probe-to-gene

• A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.

  PMID 37277355 · PMC10241789 · Nature communications · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  2232 genome-wide putative super-enhancers (SEs) were identified in mouse cranial neural crest cell (CNCC) subpopulations

  e10.5 embryonic pa2 h3k27ac promoter hi-c