REMP
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see REMP.
Repetitive Element Methylation Prediction
Bioconductor version: 3.8
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 "3.5") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, GenePrediction, ImmunoOncology, MethylationArray, Microarray, MultiChannel, Normalization, Preprocessing, QualityControl, Sequencing, Software, TwoChannel |
| Version | 1.6.1 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7 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 |
| System Requirements | |
| URL | https://github.com/YinanZheng/REMP |
| Bug Reports | https://github.com/YinanZheng/REMP/issues |
See More
| Suggests | knitr, rmarkdown, minfiDataEPIC |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | REMP_1.6.1.tar.gz |
| Windows Binary | REMP_1.6.1.zip |
| Mac OS X 10.11 (El Capitan) | REMP_1.6.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/REMP |
| Source Repository (Developer Access) | git clone [email protected]:packages/REMP |
| Bioc Package Browser | https://code.bioconductor.org/browse/REMP/ |
| Package Short Url | https://bioconductor.org/packages/REMP/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |