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TF enrichment tool
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Gene2TF: a versatile tool for detecting transcription factors underlying genes or variants in diseases


The software is developed and tested in Linux and Max OS environments.

You need BEDTools, Python 3.5, and some python packages

to run Gene2TF.

Getting Soure Code

git clone git://
cd gene2tf

Running Gene2TF


test Permutation test for enriched TFs merge Merge input ChIP-seq BED files into one

Permutation test for enriched TFs test [-h] -i INPUT_FILE [-m {empirical,kde,hypergeometric}] -o OUTPUT_PREFIX [-s {csv,tab}] [-p {ENCODE_merged.bed,H1-hESC.bed,HeLa-S3.bed,HepG2.bed,K562.bed,LCL.bed,GM12878.bed,A549.bed,HEK293.bed,MCF-7.bed,ALL}] [--path PATH] [-u UPSTREAM] [-d DOWNSTREAM] [-t THREAD] [-n NUMBER] [--background BACKGROUND] [-b {protein_coding,noncoding,pseudogene,all}] [-l LOG_FILE]

Input data

Gene2TF will calculate the TF enrichment results from input genes. Some support data is needed, that needs to be set up prior Gene2TF execution.

The gist of Gene2TF input is:

  • database (an example is
  • results (such aswhich are just randomly generated)
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