Analysis Instructions

Init Container

Startup the rstudio container in an envoironment of your choice.

Analysis

• Analysis requires a pre-requisite cell atlas model for RCTD to run correctly. We used GSE157079 for this analysis, specifically P0 adult counts and clusters
• Assuming spatial data has been process via a 10x or 10x like file structure, the files for each sample should be arranged as barcode, features and matrix .tsv.gz files in _dge suffixed folders. Adjust the folder names in the setup paths sections of run_rctd_sample.R to reflect where the source data resides
• Run run_rctd_sample.R. This will create an RCTD rds object
• Adjust the setup paths in puck_analysis.R
• Run puck_analysis.R, This will generate QC plots at the puck/bead level for all samples and dump and data and plots in the corresponding output directories
• Adjust the setup paths in gene_analysis.R
• Run gene_analysis.R, This will generate a seurat object for all samples, generate QC plots at the gene level for all samples and dump and data and plots in the corresponding output directories
• To run differential analysis between pucks, edit gen_deseq2.R for the required comparison and run. This script will output the deseq2 results for further analysis