Downstream analysis

Cellsnake provides RDS files for downstream analysis.

The RDS files are saved in the analyses or analyses_integrated directories.

The RDS files can be loaded into R using the readRDS function.

For example, to load the Seurat object for the analysis with 10% MT threshold and 0.8 resolution, use the following command:

library(Seurat)
seurat_object <- readRDS("analyses/processed/percent_mt~10/resolution~0.8/sample_name.rds")
#integrated equivalent of this command is

seurat_object <- readRDS("analyses_integrated/processed/percent_mt~auto/resolution~0.8/integrated.rds")

Annotation of cell types for this same dataset can be found in the analyses/singler directory.

library(Seurat)
singler_predictions <- readRDS("analyses/singler/percent_mt~10/resolution~0.8/sample_name.rds")

Kraken2 predictions (metagenomics results) for this same dataset can be found in the analyses/kraken directory.

library(Seurat)
kraken_predictions <- readRDS("analyses/kraken/0_3/percent_mt~10/resolution~0.8/sample_name/microbiome-full-genus-level.rds") #genus level predictions