Introduction

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

Prerequisites

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

You need BEDTools, Python 3.5, and some python packages

• numpy
• tqdm
• argparse

to run Gene2TF.

Getting Soure Code

git clone git://github.com/dolittle007/gene2tf.git
cd gene2tf

Running Gene2TF

Subcommand

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

Permutation test for enriched TFs

gene2tf.py 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)