The wheat integrative regulatory network project

This repo contains customized codes in the wheat integrative regulatory network (wGRN) project. Codes are grouped into multiple folders with appropriate comments and user manuals.

Requirements

All softwares listed in system requirements could be downloaded and installed following instructions on their offical websites.

fastp(v0.20.0) kallisto(v0.46.0) tximport(v1.12.3) BWA-mem(v0.7.15) SAMTools(v1.9) MACS2(v2.1.2) GENIE3(v1.6.0) MEME(v5.0.5) R(v3.6) GeneTribe(v1.2.0) python(v3.6.8)

Brief description of code in each folder

independent_GRN: Construction workflow of independent GRNs.
integrate_wGRN: Inference workflow of integrative networks.

Webserver

The wheat integrative network (wGRN) was integrated in a user-friendly webserver for guiding functional gene discovery.