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
Runs CellRanger on raw fastq files, basic filtering, batch correction and initial clustering
Runs SoupX on individual samples to remove ambient RNA
Runs Scrublet to model and remove doublets from individual samples
Clean up the data and perform final clustering
Generates pseudo-bulk matrices for each cluster to perform differential expression analyses
Instructions to format final Seurat object into an Azimuth reference