HPAP scRNA-seq Analysis Pipeline

Here you can find all the code used to generate data and figures in our manuscript using publically available pancreatic islet scRNA-seq data from the Human Pancreas Analysis Program (HPAP).

Raw data and interactive web browsers can be found at www.isletgenomics.org

Please cite our pipelines at: Elgamal RM et al. A reference map of cell type-specific gene expression in pancreatic islets in physiology and disease. BioRxiv 2023. doi:https://doi.org/10.1101/2023.02.03.526994

Step 1: HPAP-Initial-Clustering.R

Runs CellRanger on raw fastq files, basic filtering, batch correction and initial clustering

Step 2: HPAP-SoupX.R

Runs SoupX on individual samples to remove ambient RNA

Step 3: HPAP-Scrublet.R

Runs Scrublet to model and remove doublets from individual samples

Step 4: HPAP-Post-Processing.R

Clean up the data and perform final clustering

Step 5: HPAP-DESeq.R

Generates pseudo-bulk matrices for each cluster to perform differential expression analyses

Bonus: HPAP-Azimuth-Reference.R

Instructions to format final Seurat object into an Azimuth reference