REMP

DOI: 10.18129/B9.bioc.REMP    

This is the development version of REMP; for the stable release version, see REMP.

Repetitive Element Methylation Prediction

Bioconductor version: Development (3.17)

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>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("REMP")

For older versions of R, please refer to the appropriate Bioconductor release.

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

Details

biocViews	DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, GenomeWideAssociation, MethylationArray, Microarray, MultiChannel, Preprocessing, QualityControl, Sequencing, Software, TwoChannel
Version	1.23.0
In Bioconductor since	BioC 3.5 (R-3.4) (5.5 years)
License	GPL-3
Depends	R (>= 3.6), SummarizedExperiment(>= 1.1.6), minfi(>= 1.22.0)
Imports	readr, rtracklayer, graphics, stats, utils, methods, settings, BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel, doParallel, parallel, foreach, caret, kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db, impute, iterators
LinkingTo
Suggests	IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, 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
Links To Me
Build Report

Package Archives

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

Source Package	REMP_1.23.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/REMP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/REMP
Package Short Url	https://bioconductor.org/packages/REMP/
Package Downloads Report	Download Stats