REMP

Repetitive Element Methylation Prediction

Bioconductor version: Release (3.19)

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 (version "4.4") and enter:


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

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, GenomeWideAssociation, MethylationArray, Microarray, MultiChannel, Preprocessing, QualityControl, Sequencing, Software, TwoChannel
Version	1.28.0
In Bioconductor since	BioC 3.5 (R-3.4) (7.5 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
System Requirements
URL	https://github.com/YinanZheng/REMP
Bug Reports	https://github.com/YinanZheng/REMP/issues

Suggests	IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC
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Build Report	Build Report

Package Archives

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

Source Package	REMP_1.28.0.tar.gz
Windows Binary (x86_64)	REMP_1.28.0.zip
macOS Binary (x86_64)	REMP_1.28.0.tgz
macOS Binary (arm64)	REMP_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/REMP
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/REMP
Bioc Package Browser	https://code.bioconductor.org/browse/REMP/
Package Short Url	https://bioconductor.org/packages/REMP/
Package Downloads Report	Download Stats