REMP
This is the development version of REMP; for the stable release version, see REMP.
Repetitive Element Methylation Prediction
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| 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 | 1.37.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 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
Follow Installation instructions to use this package in your R session.
| Source Package | REMP_1.37.0.tar.gz |
| Windows Binary (x86_64) | REMP_1.37.0.zip |
| macOS Binary (big-sur-x86_64) | REMP_1.37.0.tgz |
| macOS Binary (sonoma-arm64) | REMP_1.37.0.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 |