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:
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✨
card.svg |card.png
REMP/json (API)
NEWS
| # 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
- 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)
dnamethylationmicroarraymethylationarraysequencinggenomewideassociationepigeneticspreprocessingmultichanneltwochanneldifferentialmethylationqualitycontroldataimport
Last updated from:3f67cb82cb. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 630 | ||
| linux-devel-x86_64 | NOTE | 978 | ||
| source / vignettes | OK | 797 | ||
| linux-release-x86_64 | NOTE | 1127 | ||
| macos-release-arm64 | NOTE | 744 | ||
| macos-oldrel-arm64 | NOTE | 749 | ||
| windows-devel | NOTE | 714 | ||
| windows-release | NOTE | 702 | ||
| windows-oldrel | NOTE | 824 | ||
| wasm-release | OK | 568 |
Exports:decodeAnnotdetailsfetchRefSeqGenefetchRMSKfindRECpGgetBackendgetGM12878getILMNgetParcelInfogetREgetRECpGgetRefGeneGRannotgrooMethyinitREMPrempremp_optionsremp_resetrempAggregaterempAnnotrempBrempCombinerempImpremplotrempMrempQCremprofilerempStatsrempTemplaterempTrimsaveParcel
Dependencies:abindannotateAnnotationDbiAnnotationHubaskpassbase64beanplotBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobBSgenomebumphuntercachemcaretcigarilloclassclicliprclockcodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdiagramdigestdir.expirydoParalleldoRNGdplyre1071farverfastmapfilelockforeachformatRfutile.loggerfutile.optionsfuturefuture.applygenefiltergenericsGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2globalsgluegowergtableh5mreadhardhatHDF5Arrayhmshttrhttr2illuminaioimputeipredIRangesisobanditeratorsjsonliteKEGGRESTkernlabKernSmoothlabelinglambda.rlatticelavalifecyclelimmalistenvlocfitlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimeminfiModelMetricsmulttestnlmennetnor1mixnumDerivopensslorg.Hs.eg.dbparallellypillarpkgconfigplyrpngpreprocessCoreprettyunitspROCprodlimprogressprogressrproxypurrrquadprogR.methodsS3R.ooR.utilsR6rangerrappdirsRColorBrewerRcppRcppEigenRCurlreadrrecipesrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsrpartRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsS7scalesscrimeselectrSeqinfosettingsshapesiggenessnowSparseArraysparseMatrixStatssparsevctrsSQUAREMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitevroomwithrXMLxml2xtableXVectoryaml
Readme and manuals
Help Manual
| 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 |
