Fukushima_manuscript_notebooks

The repository contains the scripts used in the study of Taniguchi et al. to process the Cellranger output files and Velocyto loom file. Including:

The script contains sub-processing functions calling Scanpy package.
The scripts used in this study to process the Cellranger and Velocyto loom file. 3.The scripts used to generate the figures illustrated in the manuscript.

Name		Name	Last commit message	Last commit date
Latest commit History 24 Commits
Fukusima_0629_2022_integrated_with_velocity_human.ipynb		Fukusima_0629_2022_integrated_with_velocity_human.ipynb
Fukusima_0705_2022_human_subset_cellrank_remove_PBMC-Copy3.ipynb		Fukusima_0705_2022_human_subset_cellrank_remove_PBMC-Copy3.ipynb
Fukusima_0707_2022_integrated_with_velocity_human_BAL_only.ipynb		Fukusima_0707_2022_integrated_with_velocity_human_BAL_only.ipynb
Fukusima_0711_2022_CellphoneDB_human.ipynb		Fukusima_0711_2022_CellphoneDB_human.ipynb
Fukusima_Human_1007_2022_for_figures.ipynb		Fukusima_Human_1007_2022_for_figures.ipynb
Fukusima_human_0304_2022.ipynb		Fukusima_human_0304_2022.ipynb
Fukusima_scRNASeq_dorothea_integration_1006_2022.ipynb		Fukusima_scRNASeq_dorothea_integration_1006_2022.ipynb
Fukusima_visium_stlearn_0711_2022.ipynb		Fukusima_visium_stlearn_0711_2022.ipynb
README.md		README.md
Scanpy_functions_v03262021.ipynb		Scanpy_functions_v03262021.ipynb

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