Welcome to Cellsnake’s Documentation!

Cellsnake is a command line tool designed for easy and scalable single-cell analysis. It can be used as a Snakemake workflow or as a standalone command line tool.

It is build on Seurat4 but Seurat5 version is coming soon!

Our main repository location: sinanugur/cellsnake

Our Snakemake workflow location: sinanugur/scrna-workflow

Getting Started

• Installation
  • How to use the Docker Image
  • How to request higher memory and CPUs?
• Quick start example
• Example run on Fetal Brain dataset
  • Start with a dry run
  • A minimal run
  • QC
  • Run integration on seperately processed samples
  • Run a standard workflow on integrated object
  • Resolution parameter change granulation so clustering
  • Run an advanced workflow on integrated object
  • Autoresolution is also possible
• Example run on Fetal Liver dataset
  • Starting with a minimal run
  • Integration
  • Work on the integrated sample
  • We can include the metadata to compare different groups
  • Visualisation of a marker gene
• Metagenomics analysis
• How to draw marker plots
• Config Files (Parameter Files)
  • Changing the organism to mouse
• Options and Arguments
  • Modes
  • Full parameter list
• Downstream analysis
• Glossary