RED-ML RED-ML is a software tool to do genome-wide RNA editing dectection (RED) based on RNA-seq data. All source codes and executables are located in the "bin" directory. The tool can be run on a Linux platform and the main program is red_ML.pl.

Introduction

RED-ML: RNA Editing Detection basedon Machine learning (pronounced as “red ML”). The input to RED-ML can be as simple as a single BAM file, while it can also take advantage of matched genomic variant information when available. The output not only contains detected RNA editing sites, but also a confidence score to facilitate downstream filtering. The developers have carefully designed validation experiments and performed extensive comparison and analysis to show the efficiency and effectiveness of RED-ML under different conditions, and it can accurately detect novel RNA editing sites without relying on curated RNA editing databases. This tool is also freely available via GitHub <https://github.com/BGIRED/REDML.

Publications

  1. Red Ml: A Novel, Effective Rna Editing Detection Method Based On Machine Learning.
    Cite this
    Xiong H, Liu D, Li Q, Lei M, Xu L, Wu L, Wang Z, Ren S, Li W, Xia M, Lu L, Lu H, Hou Y, Zhu S, Liu X, Sun Y, Wang J, Yang H, Wu K, Xu X, Lee LJ, 2017 May 1 - Giga Science

Credits

  1. Leo J Lee ljlee@psi.toronto.edu
    Investigator

    Department of Electrical and Computer Engineering, University of Toronto, Canada

  2. Xun Xu xuxun@genomics.cn
    Investigator

    China National GeneBank, BGI-Shenzhen, China

Community Ratings

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hao***i@big.ac.cn (May 7, 2021)
Summary
AccessionBT007072
Tool TypeApplication
CategoryRNA editing
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Input DataBAM, FASTA
Latest Release1.0 (April 7, 2018)
Download Count1237
Country/RegionCanada
Submitted ByHao Lili
Fundings

This project is supported by the Shenzhen Peacock Plan (NO. KQTD20150330171505310).