GCEN++: A C++ tool for Gene Co-Expression Networks

GCEN++ 0.1.0 provides three subprograms: data_normalization, data_filter and network_construction.

Download: GCEN++_Linux_0.1.0.zip GCEN++_Windows_0.1.0.zip

Usage:

data_normalization
network_normalization -i inputfile -o outputfile
-i --input, inputfile, default: ./test/gene_expr.tsv
-o --output, outputfile, default: ./test/gene_expr_norm.tsv
-m --method, normalization method, default: upqt
-h --help, print help information
Input file format: table separate, first column are genename, the others are gene expression value
Output file format: The file structure is the same as input file

data_filter
data_filter -i input_file -o outputfile
-i --input, input file, default: ./test/gene_expr.tsv
-o --output, output file, defalut: ./test/gene_expr_filter.tsv
-m --mean, mean cutoff, defalt: 0.0
-s --std, std cutoff, defalt: 0.0
-h --help, print help information
Input file format: table separate, first column are genename, the others are gene expression value
Output file format: The file structure is the same as input file

network_construction
network_construction -i inputfile -o outputfile
-i --input, inputfile, default: ./test/sample.tsv
-o --output, outputfile, default: result.network
-m --method, correlation coefficient method, default: spearman
-p --process, cpu cores, default: 2
-h --help, print help information
Input file format: table separate, first column are genename, the others are gene expression value
Output file format: table separate, four columns are geneA, geneB, correlation coefficent, P value

Usage: