REMP
This is thereleased version of REMP; for the devel version, seeREMP.
Repetitive Element Methylation Prediction
Bioconductor version: Release (3.22)
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("REMP")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("REMP")For older versions of R, please refer to the appropriateBioconductor 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation,DataImport,DifferentialMethylation,Epigenetics,GenomeWideAssociation,MethylationArray,Microarray,MultiChannel,Preprocessing,QualityControl,Sequencing,Software,TwoChannel |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (8.5 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,Seqinfo,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 |
See More
| Suggests | IlluminaHumanMethylation450kanno.ilmn12.hg19,IlluminaHumanMethylationEPICanno.ilm10b2.hg19,BSgenome.Hsapiens.UCSC.hg19,BSgenome.Hsapiens.UCSC.hg38,knitr,rmarkdown,minfiDataEPIC |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | REMP_1.34.0.tar.gz |
| Windows Binary (x86_64) | REMP_1.34.0.zip |
| macOS Binary (x86_64) | REMP_1.34.0.tgz |
| macOS Binary (arm64) | REMP_1.34.0.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 |