scRNA-seq analysis for Radhouani et al. paper, Science Immunology, 2025.
The running order of the scripts is as follows:
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Reading the data in R using:
- R/1_read_in_pilot.Rmd
- R/2_read_in_final.Rmd
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Performing single-cell integration using scVI, initial annotation using scNym, and leiden clustering of mature and hematopoietic stem cells (HSC).
- python/1_scvi_integration.ipynb
- python/2_scnym_annotation.ipynb
- python/3_clustering_for_manual_annotation.ipynb
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Marker detection of the clusters.
- R/3_hvg_DEGs_HSC_scnym_annotation.Rmd
- R/4_hvg_DEGs_mature_scnym_annotation.Rmd
These markers have been used for manual annotation of the clusters.
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Transfer and plotting of the data with manually annotated clusters. This script relies on python/4_dynamo_cell_cycle.ipynb for cell cycle annotation.
- python/5_transfering_manual_annotation.ipynb
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Differential expression between SA- and PBS-treated mice across cell types.
- R/5_DEGs_HSC_scnym_annotation_manual_annotation.Rmd
- R/6_DEGs_mature_scnym_annotation_manual_annotation.Rmd
