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
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Repetitive Element Methylation Prediction
Bioconductor version: Release (3.5)
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")
| R Script | An Introduction to the REMP Package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, GenePrediction, MethylationArray, Microarray, MultiChannel, Normalization, Preprocessing, QualityControl, Sequencing, Software, TwoChannel |
| Version | 1.0.7 |
| 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_1.0.7.tar.gz |
| Windows Binary | REMP_1.0.7.zip |
| Mac OS X 10.11 (El Capitan) | REMP_1.0.7.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/REMP |
| Package Short Url | http://bioconductor.org/packages/REMP/ |
| Package Downloads Report | Download Stats |
Documentation »
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