To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("REMP")

In most cases, you don't need to download the package archive at all.

REMP

DOI: 10.18129/B9.bioc.REMP    

Repetitive Element Methylation Prediction

Bioconductor version: Release (3.6)

Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE.

Author: Yinan Zheng [aut, cre], Lei Liu [aut], Wei Zhang [aut], Warren Kibbe [aut], Lifang Hou [aut, cph]

Maintainer: Yinan Zheng <y-zheng at northwestern.edu>

Citation (from within R, enter citation("REMP")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("REMP")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("REMP")

 

PDF R Script An Introduction to the REMP Package
PDF   Reference Manual
Text   NEWS

Details

biocViews Alignment, DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, GenePrediction, MethylationArray, Microarray, MultiChannel, Normalization, Preprocessing, QualityControl, Sequencing, Software, TwoChannel
Version 1.2.1
In Bioconductor since BioC 3.5 (R-3.4) (0.5 years)
License GPL-3
Depends R (>= 3.4), SummarizedExperiment(>= 1.1.6), minfi(>= 1.22.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19
Imports graphics, stats, utils, methods, settings, BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges, BiocParallel, doParallel, parallel, foreach, caret, kernlab, ranger, BSgenome, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, org.Hs.eg.db, impute, iterators
LinkingTo
Suggests knitr, rmarkdown, minfiDataEPIC
SystemRequirements
Enhances
URL https://github.com/YinanZheng/REMP
BugReports https://github.com/YinanZheng/REMP/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package REMP_1.2.1.tar.gz
Windows Binary REMP_1.2.1.zip
Mac OS X 10.11 (El Capitan) REMP_1.2.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/REMP
Package Short Url http://bioconductor.org/packages/REMP/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.6 Source Archive

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