MSC_BM_scripts

How to get the data?

Download the data from GEO install Python scanpy, loompy and all the other Python packages loaded in the Load_GEO_data_analyze_it.ipynb, copy the Python Jupyter notebook and run that.

How did we analyze the data?

Here we present the scripts used to process the MSC_BM data published on the NCBI GEO GSE190965 as well as BioRxiv.

All script are in the scripts sub-folder, both as python notebooks (.ipynb) and html pages. Due to inline graphics these are too big to show here. You need to download them and load the local copies.

The data has been processed in three steps:

1. Combining the loom files created during mapping of the data using kallist/bustools filtering and normalization: Hongze_healthy_2020_10_merged
2. 2D UMAP, clustering and downstream analysis: Hongze_healthy_2020_10_merged_2D
3. Figures and analyses for the paper: 20220328revision
4. Removal of doublets DubletSearch
5. Analysis of doublet removed data DoubletRemoved
6. The Female vs male comparison Female_male20220316