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Teichlab
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Pan_fetal_immune
Collection of scripts for analysis of pan fetal immune atlas
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Code / data availability checklist
#46
Closed
emdann
closed
2 years ago
emdann
commented
2 years ago
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
Pre-submission
[x] Make repository public
Post-submission