Analysis Instructions

Init Container

Startup the rstudio container in an envoironment of your choice.

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