generate gct file (version 1.2, for GSEA or ssGSEA) from gene expression matrix file
Project description
expr2gct
generate gct file (version 1.2, for GSEA or ssGSEA) from gene expression matrix file. note that gene expression matrix file should be tab delimited file.
Installation
install from pip
$ pip install expr2gct
install from source
$ git clone https://github.com/sxropensource/expr2gct.git
$ cd expr2gct
$ python setup.py install
Usage
$ expr2gct --help
usage: expr2gct [-h] -e EXPR [-d DESC] -g GCT
optional arguments:
-h, --help show this help message and exit
-e EXPR, --expr EXPR Gene expression matrix file(tab delimited only), first
row is sample names, first column is gene symbols
-d DESC, --desc DESC gct file need DESCRIPTION for column 2 for every gene,
If not provided, default use gene symbol(column 1)
instead. Note that if you provide a DESCRIPTION file,
every row reprents a gene. eg, the first row in
DESCRIPTION file represents the first gene in
expression file.
-g GCT, --gct GCT Where to save gct file
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expr2gct-1.0.0.tar.gz
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