Published October 26, 2023
| Version v2
Model
Open
Human breast cell atlas - single cell RNA cell type annotation models and singularity
Authors/Creators
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1.
University of Cambridge
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2.
Wellcome/MRC Cambridge Stem Cell Institute
Contributors
Researcher (2):
Supervisor (2):
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1.
European Bioinformatics Institute
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2.
University of Cambridge
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3.
Wellcome/MRC Cambridge Stem Cell Institute
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4.
Genentech
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5.
Cancer Research UK Cambridge Institute
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6.
Wellcome Sanger Institute
Description
Created as part of the integrated Human Breast Cell Atlas (iHBCA), we present seven independent CellTypist linear regression models for simple label transfer from any of the seven labelled datasets part of our atlas. These should allow quick and easy cell type label transfer to new single cell RNA sequencing data sets through the CellTypist software (Conde et al., 2022).
Additionally, we present the singularity container (singularity_sc_v0.2.3.def) used in scanpy and batch integration (scVI) workflows used to generate the HBCA and iHBCA datasets (see https://github.com/MarioniLab/hbca).
Files
Files
(3.9 MB)
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Additional details
Software
- Repository URL
- https://github.com/MarioniLab/hbca
- Programming language
- Python , R