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).

• MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions.

  PMID 36451166 · PMC9710047 · Genome biology · 2022 · 7 claims · 6 setups

  Has reproduction · 50

  MoDLE is a high-performance stochastic model that simulates DNA-DNA contacts from loop extrusion genome-wide in minutes using less than 1 GB of RAM

  genome synthetic h1-hesc stochastic molecular ctcf

• snpQT: flexible, reproducible, and comprehensive quality control and imputation of genomic data.

  PMID 34900230 · PMC8637247 · F1000Research · 2021 · 8 claims · 4 setups

  Has reproduction · 67

  snpQT is a scalable, stand-alone software pipeline using nextflow and BioContainers for comprehensive, reproducible, interactive QC of human genomic data.

  synthetic amyotrophic user snp-array gwas population

• Viewing RNA-seq data on the entire human genome.

  PMID 28979763 · PMC5605993 · F1000Research · 2017 · 6 claims · 3 setups

  Has reproduction · 50

  RNA-Seq Viewer is a web application that visualizes genome-wide expression data from NCBI's SRA and GEO databases using an ideogram across the entire human genome.

  homo genome chrome rna-seq genomic web-page

• MirDIP 5.2: tissue context annotation and novel microRNA curation.

  PMID 36453996 · PMC9825511 · Nucleic acids research · 2023 · 7 claims · 6 setups

  Has reproduction · 89

  mirDIP 5.2 removed eight outdated resources, added miRNATIP, and ran five prediction algorithms against miRBase and mirGeneDB miRNAs to expand and improve interaction coverage

  mirnas disease novel type mirna small bulk