Cistrome-GO 1.0.0

Functional enrichment analysis of transcription factor ChIP-seq peaks. The package of http://go.cistrome.org.

Requirements

This software is based on python2.7, some python packages are required.

• xlmhg==2.4.9
• mne==0.17.0
• scipy

Installation

git clone https://github.com/WChangson/Cistrome-GO.git
cd Cistrome-GO
python setup.py install

Usage

For all the help information, please input

cistromego --help

Solo mode of Cistrome-GO

cd test_data
cistromego -g hg38 -b MYOD1.bed

Ensemble mode of Cistrome-GO

cd test_data
cistromego -g hg38 -b peak.bed -e de.txt

• -v/--version

Check the version of Cistrome-GO you are using.

• -g/--genome

Specify your genome assembly, select from hg38, hg19, mm10, mm9.

• -b/--bed

Peak bed file path.

• -pn/--peaknumber

Top peak number to use for analysis. Set all to use all the peaks. By default is 10000.

• -d/--decay

Half decay distance to use. Select from auto, 0.5k, 1k, 10k, 50k, 100k, 500k. By default is auto.

• -n/--name

Specify the prefix of your output file.

• -o/--output

Specify the output directory of your result. The program will create it if it does not exists. By default is current directory.

• -dg/--dego

upgenes, downgenes, allgenes for gene ontology. By default is allgenes.

• -e/--expr

Expression file path. If users input this parameter, Cistrome-GO will run as ensemble mode.

• -ei/--exprinfo

Expression file format setting. Column index of geneID, logFoldChange, FDR in differential expression file. By default: 1,3,7.

• -max/--maxgenenumber

Maximum gene number in the GO or kegg terms. By default: 2000.

• -min/--mingenenumber

Minimum gene number in the GO or kegg terms. By default: 10.

• -logfc/--logfccut

logFoldChange of differential expression genes. By default: 1.0.

• -fdr/--fdrcut

FDR cutoff of differential expression genes. By default: 0.05.