https://github.com/brickmanlab/simon-et-al-2024

https://github.com/brickmanlab/simon-et-al-2024

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • CITATION.cff file
  • codemeta.json file
    Found codemeta.json file
  • .zenodo.json file
  • DOI references
    Found 4 DOI reference(s) in README
  • Academic publication links
    Links to: biorxiv.org, ncbi.nlm.nih.gov, zenodo.org
  • Academic email domains
  • Institutional organization owner
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (1.3%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: brickmanlab
  • Language: Python
  • Default Branch: master
  • Size: 3.91 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme

README.md

Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst

Simon et al. (2025)

Analysis notebooks for Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst

Owner

  • Name: Brickman group
  • Login: brickmanlab
  • Kind: organization
  • Location: Copenhagen

Professor Joshua Brickman at Center for Stem Cell Medicine (reNEW), University of Copenhagen

GitHub Events

Total
  • Public event: 1
  • Push event: 4
  • Create event: 2
Last Year
  • Public event: 1
  • Push event: 4
  • Create event: 2

Dependencies

requirements.txt pypi
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