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generate gct file (version 1.2, for GSEA or ssGSEA) from gene expression matrix file

Project description


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.


install from pip

$ pip install expr2gct

install from source

$ git clone
$ cd expr2gct
$ python install


$ 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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