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crispr-mageck-nf

Statistical analysis of CRISPR and shRNA functional genetic screening data using MAGeCK.

Installation

Nextflow

Install nextflow following the instructions at https://www.nextflow.io/docs/latest/getstarted.html

Singularity

Install singularity following the instructions at https://singularity.lbl.gov/install-linux

crispr-mageck-nf pipeline

The most convenient way is to install crispr-mageck-nf is to use nextflow's built-in pull command

nextflow pull zuberlab/crispr-mageck-nf

Test

Before you start, make sure nextflow and singularity are properly installed on your system.

Clone git repository from Github and run the pipeline using the provided test data.

git clone https://github.com/ZuberLab/crispr-mageck-nf.git
cd crispr-mageck-nf
./test

Documentation

nextflow run zuberlab/crispr-mageck-nf --help

Credits

Nextflow: Paolo Di Tommaso - https://github.com/nextflow-io/nextflow

Singularity: Singularityware - https://singularity.lbl.gov

MAGeCK: Wei Li / Shirley Liu - http://mageck.sourceforge.net