pycrispr

pycrispr: a scalable and reproducible pipeline for analysing CRISPR-Cas9 screen data. It implements the snakemake workflow management system.

Experimental considerations

• Model system
• sgRNA library selection
• sgRNA library transduction and representation
• Sample comparisons
• Protocols
• References

Getting started with pycrispr

• Requirements
  • Hardware
  • Software
• Installation
  • 1. Conda/Mamba installation
  • 2. Installation of snakemake
  • 3. Installation of pycrispr

Running pycrispr

• User guide
  • All options
  • Getting started with pycrispr
  • Preparing CRISPR-Cas9 screen data
  • Initiating the pipeline
  • Output files
  • Report

Project information

• Citation
  • APA
  • BibTeX
  • Zenodo DOI
• About pycrispr

Links

• Source code

• Report an issue

• Project page on PyPi

• Paul Lehner lab website

• James Nathan lab website