Description

Mageck test performs a robust ranking aggregation (RRA) to identify positively or negatively selected genes in functional genomics screens.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

count_table:file

Count table file. Each line in the table should include sgRNA name (1st column), target gene (2nd column) and read counts in each sample.

*.{txt,tsv}

Output

name:type
description
pattern

gene_summary

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.gene_summary.txt:file

Gene summary file describing the fitness score and associated p-values.

*.{gene_summary.txt}

sgrna_summary

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.sgrna_summary.txt:file

sgRNA summary file describing the sgRNA and associated gene

*.{sgrna_summary.txt}

r_script

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.R:file

R script allowing to output plots from main hit genes

*.R

versions

versions.yml:file

File containing software versions

versions.yml

Tools

mageck
BSD License

MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data.

sourceforge.net/p/mageck/wiki/Home/#mle sourceforge.net/p/mageck/wiki/Home https://bitbucket.org/liulab/mageck/src 10.1186/s13059-015-0843-6
included in
crisprseq
maintainer
Github user LaurenceKuhl
get in touch
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