Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
bios4biol
bioinfo-utils
Commits
7bdf1b93
Commit
7bdf1b93
authored
Aug 09, 2016
by
Claire Hoede
Browse files
Differencial analysis of expression
parent
d69159a9
Changes
1
Hide whitespace changes
Inline
Side-by-side
bin/DEG.R
View file @
7bdf1b93
##NAME = "DEG.R"
##SYNOPSIS = "DEG.R |-f <raw_data_path>/<file_name>.csv -n <normalized_factor_path>/<file_name>.csv -o <results_path> --pool1 lib1,lib2... --pool2 lib3,lib4... --filter true or false --correct "bonferroni" or "BH" --MAplots true or false --alpha 0.05"
##EXAMPLE = "Rscript --vanilla DEG.R --file './data/count_table.csv' --norm './Normalization/RLE_info.txt' --pool1 'untreated1,untreated2,untreated3,untreated4' --pool2 'treated1,treated2,treated3' --MAplots 'FALSE' --alpha 0.05 --filter TRUE --correct 'BH' --out './results/'"
##DATE = "03/2016"
##AUTHORS = "Gaëlle Lefort"
##KEYWORDS = "RNAseq differentially expressed genes"
##DESCRIPTION = "DEG.R imports data, converts them into a DGEList object (edgeR), does tests to find differentially expressed genes and produces diagnostic plots."
##################### Differential Analysis Expression #########################
################################################################################
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment