Processing pipeline for nPOD multi-modal project

Here you can find all the code used to generate data and downstream analysis in our manuscript using snATAC-seq, snRNA-seq, and multiome data from the network for pancreatic donors with diabetes (nPOD).

All raw data for this project are available under the Bioproject accession number: PRJNA1141467

We have created online browsers for easy accessibility: http://tools.cmdga.org:3838/npod-whole-pancreas

Data processing

data preprocessing

For information regarding data preprocessing refer to data_preprocessing.md in data processing directory. This will include information regarding running cellranger for all modalities and window based matrix creation for chromatin data.

initial sample processing

For information regarding initial qc filtering and merging/clustering data refer to data_processing.md in the data processing directory.

downstream analysis

For information regarding the analysis performed for this project refer to downstream_analysis.md in the downstream analysis directory.