Package: REMP 1.37.0

Yinan Zheng

REMP: Repetitive Element Methylation Prediction

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.

Authors:Yinan Zheng [aut, cre], Lei Liu [aut], Wei Zhang [aut], Warren Kibbe [aut], Lifang Hou [aut, cph]

REMP_1.37.0.tar.gz
REMP_1.37.0.zip(r-4.7)REMP_1.37.0.zip(r-4.6)REMP_1.37.0.zip(r-4.5)
REMP_1.37.0.tgz(r-4.6-any)REMP_1.37.0.tgz(r-4.5-any)
REMP_1.37.0.tar.gz(r-4.7-any)REMP_1.37.0.tar.gz(r-4.6-any)
REMP_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
REMP/json (API)

# Install 'REMP' in R:

install.packages('REMP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yinanzheng/remp/issues

Datasets:

Alu.hg19.demo - Subset of Alu genomic location dataset
Alu.hg38.demo - Subset of Alu genomic location dataset

On BioConductor:REMP-1.37.0(bioc 3.24)REMP-1.36.0(bioc 3.23)

dnamethylation microarray methylationarray sequencing genomewideassociation epigenetics preprocessing multichannel twochannel differentialmethylation qualitycontrol dataimport

6.52 score 3 stars 31 scripts 4 mentions 31 exports 188 dependencies

Last updated from:3f67cb82cb. Checks:1 WARNING, 6 NOTE, 2 OK, 1 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	592
linux-devel-x86_64	NOTE	955
source / vignettes	OK	797
linux-release-x86_64	NOTE	981
macos-release-arm64	NOTE	502
macos-oldrel-arm64	NOTE	562
windows-devel	NOTE	757
windows-release	ERROR	685
windows-oldrel	NOTE	822
wasm-release	OK	582

Exports:decodeAnnot details fetchRefSeqGene fetchRMSK findRECpG getBackend getGM12878 getILMN getParcelInfo getRE getRECpG getRefGene GRannot grooMethy initREMP remp remp_options remp_reset rempAggregate rempAnnot rempB rempCombine rempImp remplot rempM rempQC remprofile rempStats rempTemplate rempTrim saveParcel

Dependencies:abind annotate AnnotationDbi AnnotationHub askpass base64 beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel BiocVersion Biostrings bit bit64 bitops blob BSgenome bumphunter cachem caret cigarillo class cli clipr clock codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats diagram digest dir.expiry doParallel doRNG dplyr e1071 farver fastmap filelock foreach formatR futile.logger futile.options future future.apply genefilter generics GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 globals glue gower gtable h5mread hardhat HDF5Array hms httr httr2 illuminaio impute ipred IRanges isoband iterators jsonlite KEGGREST kernlab KernSmooth labeling lambda.r lattice lava lifecycle limma listenv locfit lubridate magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime minfi ModelMetrics multtest nlme nnet nor1mix numDeriv openssl org.Hs.eg.db parallelly pillar pkgconfig plyr png preprocessCore prettyunits pROC prodlim progress progressr proxy purrr quadprog R.methodsS3 R.oo R.utils R6 ranger rappdirs RColorBrewer Rcpp RcppEigen RCurl readr recipes rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools rpart Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors S7 scales scrime selectr Seqinfo settings shape siggenes snow SparseArray sparseMatrixStats sparsevctrs SQUAREM statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs viridisLite vroom withr XML xml2 xtable XVector yaml

An Introduction to the REMP Package

Introduction | Installation | REMP: Repetitive Element Methylation Prediction | Extract RE-CpG methylation profiled by Illumina BeadChip array

Rendered fromREMP.Rnwusingutils::Sweave

Last update: 2020-04-12
Started: 2017-01-24

Help page	Topics
Repetitive Element Methylation Prediction	REMP-package REMP
Subset of Alu genomic location dataset (hg19)	Alu.hg19.demo
Subset of Alu genomic location dataset (hg38)	Alu.hg38.demo
Get RefSeq gene database	fetchRefSeqGene
Get RE database from RepeatMasker	fetchRMSK
Find RE-CpG genomic location given RE ranges information	findRECpG
Get BiocParallel back-end	getBackend
Get methylation data of HapMap LCL sample GM12878 profiled by Illumina 450k array or EPIC array	getGM12878
Annotate genomic ranges data with gene region information.	GRannot
Groom methylation data to fix potential data issues	grooMethy
RE Annotation Database Initialization	initREMP
Repetitive element methylation prediction	remp
Set or get options for REMP package	remp_options remp_reset
REMParcel instances	getILMN getILMN,REMParcel-method getParcelInfo getParcelInfo,REMParcel-method getRE getRE,REMParcel-method getRECpG getRECpG,REMParcel-method getRefGene getRefGene,REMParcel-method REMParcel REMParcel-class saveParcel saveParcel,REMParcel-method
REMProduct instances	decodeAnnot decodeAnnot,REMProduct-method details details,REMProduct-method rempAggregate rempAggregate,REMProduct-method rempAnnot rempAnnot,REMProduct-method rempB rempB,REMProduct-method rempCombine rempCombine,REMProduct,REMProduct-method rempImp rempImp,REMProduct-method remplot remplot,REMProduct-method rempM rempM,REMProduct-method rempQC rempQC,REMProduct-method REMProduct REMProduct-class rempStats rempStats,REMProduct-method rempTrim rempTrim,REMProduct-method
Extract DNA methylation data profiled in RE	remprofile
Prepare data template for REMP	rempTemplate

Package: REMP 1.37.0

REMP: Repetitive Element Methylation Prediction

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)