LncDM:An R package for performing DNA methylation pattern of lncRNAs based on a reannotation method

Introduction

LncDM is a novel computational method for identifying different methylation site,different methylation region and different methylation element in specific disease.Here we provide multiple options for user to analyze protein coding gene,lincRNA and other long non-coding RNA,pseudogene.LncDM is based on reannotation method to use Illumina HumanMethylation450 BeadChip and Gencode's all annotation information,and get different transcript's CpG value.We consider gene function region to caculate DM pattern.LncDM provide several test options and threshold value for users.Users can get data visualization in many aspects.

Installation

1.The LncDM package requires R version >= 3.30 .

2.The LncDM package requires the following packages to be installed: beanplot,reshape,gplots,WriteXLS,MASS,impute,limma,preprocessCore. If your system does not have them installed, the easiest way to install them is to issue the following command at the R prompt: source("http://bioconductor.org/biocLite.R"); biocLite(c("impute","limma","preprocessCore")); install.packages(c("beanplot","reshape","gplots","WriteXLS","MASS"),repos="http://cran.r-project.org");

3.Install LncDM package: install.packages("LncDM", repos="http://R-Forge.R-project.org");

Tutorial

A vignentte that illustrate various aspects of LncDM is available here

The user manual of LncDM package could be found here

The project summary page you can find here.

Author: Hui Zhi<zhihui013201@gmail.com>