Description

maximum-likelihood analysis of gene essentialities computation

Input

Name (Type)
Description
Pattern

meta (map)

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

]

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}

design_matrix (file)

Design matrix describing the samples and conditions

*.{txt,tsv}

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

gene_summary (file)

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

*.{gene_summary}

sgrna_summary (file)

sgRNA summary file describing the sgRNA and
associated gene

*.{gene_summary}
included in
crisprseq
author
Github user LaurenceKuhl
get in touch
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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