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RegOmics

Description

This repository is the code source for the RegOmics (Regulatory extraction for Omics data) tool for identifying transcription (TF) - target relations and suggesting potential TF candidates in user-uploaded data. This work belongs to the Chapter 4 of my PhD thesis.

RegOmics is able to operate with the long list of genes/proteins derived from omic data. This tool can identify the TF-target relations that existed in the user input data, can rank these TF-target relations, and could suggest candidate TFs to researchers

RegOmics is also available as a web-based version https://nhannguyen.shinyapps.io/RegOmics_Rshinyapp/.

Instructions

  • The code folder stores all R separated functions that are used in the RegOmics pipeline
  • The example folder stores some example files to run in the RegOmics tool
  • The reference folder stores the default TF-target relation databases
  • The pipeline file is run the the RegOmics pipeline as an R script.
  • The RegOmics_Rshinyapp folder stores all source code and setting for the online RegOmics Rshiny app. Users also could download this folder and run the app at a local computer.

Contact:

LinkedIn: nhannguyen | ORCID: 0000-0001-8720-1195