Package: REMP Type: Package Title: Repetitive Element Methylation Prediction Version: 1.37.0 Authors@R: c(person("Yinan","Zheng", role = c("aut","cre"), email = "y-zheng@northwestern.edu"),person("Lei","Liu", role = c("aut"), email = "lei.liu@northwestern.edu "), person("Wei","Zhang", role = c("aut"), email = "wei.zhang1@northwestern.edu"), person("Warren","Kibbe", role = c("aut"), email = "warren.kibbe@nih.gov"), person("Lifang","Hou", role = c("aut","cph"), email = "l-hou@northwestern.edu")) Description: 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. 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 Suggests: IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, minfiDataEPIC Collate: REMParcel-class.R REMProduct-class.R generics.R REMParcel-methods.R REMProduct-methods.R options.R utils.R REMPtools.R getGM12878.R grooMethy.R initREMP.R rempTemplate.R remp.R remprofile.R DemoData.R onAttach.R REMP-package.R URL: https://github.com/YinanZheng/REMP BugReports: https://github.com/YinanZheng/REMP/issues Encoding: UTF-8 LazyData: true biocViews: DNAMethylation, Microarray, MethylationArray, Sequencing, GenomeWideAssociation, Epigenetics, Preprocessing, MultiChannel, TwoChannel, DifferentialMethylation, QualityControl, DataImport RoxygenNote: 7.1.2 Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 12:45:06 UTC RemoteUrl: https://github.com/bioc/REMP RemoteRef: HEAD RemoteSha: 3f67cb82cbd7f86153850f9e843aa3d18d82ddbf NeedsCompilation: no Packaged: 2026-07-04 02:20:10 UTC; root Author: Yinan Zheng [aut, cre], Lei Liu [aut], Wei Zhang [aut], Warren Kibbe [aut], Lifang Hou [aut, cph] Maintainer: Yinan Zheng