Code / data availability checklist

[emdann]

Pre-submission

• [x] Are all bits of analysis in the code repository?
  • [x] Missing script/code to run cpdb analysis (can be a .sh)
    • [x] Missing scripts for preprocessing TCR/BCR data: scirpy and dandelion analysis code (to generate ​​/lustre/scratch117/cellgen/team297/kt16/panfetal/PAN.A01.v01.entire_data_normalised_log.20210429.LYMPHOID.embedding_dandelion_productive.csv)
    • [x] Identification of maternal contaminants: souporcell call + scripts
• [x] Add conda environment yaml: one for scvi-tools and one for CPU analysis
• [x] Data portal up and running
  • [x] download links
  • [x] cellxgene links
  • [x] high res img links
• [x] Check links to data in repository README
• [x] Add example notebooks:
  • [x] Visium data exploration
  • [x] scArches mapping
• [x] Transfer repository to TeichLab https://docs.github.com/en/repositories/creating-and-managing-repositories/transferring-a-repository#transferring-a-repository-owned-by-your-user-account

• [x] Make repository public

  Post-submission

• [x] Add link to biorxiv
• [x] Contact DCP wrangling team