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DOI: 10.18129/B9.bioc.REMP    

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>

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PDF R Script An Introduction to the REMP Package
PDF   Reference Manual
Text   NEWS


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,, impute, iterators
Suggests knitr, rmarkdown, minfiDataEPIC
Depends On Me
Imports Me
Suggests Me
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