Download raw data

Download 10x snATAC-seq raw data from NCBI Gene Expression Omnibus (GSE169453) Download 10x multiome raw data from NCBI Gene Expression Omnibus (GSE200044)

Download processed data to reproduce figures

1, download files less than 25M from github data folder:

https://github.com/gaoweiwang/Islet_snATACseq

2, download files from figshare:

multiome: https://figshare.com/articles/dataset/processed_multiome_zip/19497665 snATACseq: https://figshare.com/articles/dataset/processed_snATACseq_zip/19497656

3, download large files:

snATAC-seq data (http://169.228.232.194/~mmallick/o/processed_snATACseq.tar.gz) multiome data (http://169.228.232.194/~mmallick/o/processed_multiome.tar.gz)

Figures:

Use the cell_clustering.ipynb notebook to reproduce cell clustering results Use the downstream_analysis.ipynb notebook to reproduce downstream analyses

Scripts:

Use AI_Hypothesis_testing.ipynb to train classifier to distinguish beta cells from ND, pre-T2D and T2D donors Use AI_subtype.ipynb to train classifier to distinguish beta cell subtypes enriched in ND and T2D donors Use AI_HPAP.ipynb to predict subtype of beta cells from public HPAP isle snATAC-seq dataset Use run_scWASP.py and run_imbalance.py to perform genetic analysis

Session information

Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
attached base packages:
grid stats4 parallel stats graphics grDevices utils datasets methods base