Quick start example

Run cellsnake in a clean directory and cellsnake will create the required directories while running.

After downloading the dataset, just point the data folder which contains the two dataset folders, this will trigger a standard cellsnake workflow:

cellsnake standard data
# -j argument is optional, it will speed up the pipeline via threading, for example
cellsnake standard data -j 5

After the pipeline finishes, you may also integrate these two samples:

cellsnake integrate data

There will be a file called integrated.rds in the analyses_integrated/seurat folder. This file can be used for further analysis after integration.

Let’s say you want a resolution of 0.1, then you can trigger a run with this resolution.

cellsnake integrated standard analyses_integrated/seurat/integrated.rds --resolution 0.1

To determine a manual resolution parameter, you can also create only a ClusTree.

cellsnake integrated clustree analyses_integrated/seurat/integrated.rds

It is also possible to use automatic resolution selection, however this might be very slow in large datasets.

cellsnake integrated standard analyses_integrated/seurat/integrated.rds --resolution auto