Package: DMRcate 3.1.4

Tim Peters

DMRcate: Methylation array and sequencing spatial analysis methods

De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.

Authors:Tim Peters

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NEWS

# Install 'DMRcate' in R:

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

On BioConductor:DMRcate-3.1.2(bioc 3.20)DMRcate-3.0.3(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

14 exports 2.05 score 210 dependencies 1 dependents 132 mentions

Last updated 13 days agofrom:e37173a4b5

Exports:changeFDR cpg.annotate DMR.plot dmrcate extractCoords extractRanges fitParallel KernelSums KernelTest rmPosReps rmSNPandCH Segment sequencing.annotate SparseDeltas

Dependencies:abind annotate AnnotationDbi AnnotationFilter AnnotationHub askpass backports base64 base64enc beachmat beanplot BH BiasedUrn Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib bsseq bumphunter cachem checkmate cli clipr cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats deldir dichromat digest doRNG dplyr edgeR ensembldb evaluate ExperimentHub fansi farver fastmap FDb.InfiniumMethylation.hg19 filelock fontawesome foreach foreign formatR Formula fs futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue GO.db gridExtra gtable gtools Gviz HDF5Array highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno.ilm10b4.hg19 IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICv2anno.20a1.hg38 IlluminaHumanMethylationEPICv2manifest illuminaio interp IRanges isoband iterators jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise methylumi mgcv mime minfi missMethyl multtest munsell nlme nnet nor1mix openssl org.Hs.eg.db permute pillar pkgconfig plogr plyr png preprocessCore prettyunits progress ProtGenerics purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl readr reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rngtools rpart Rsamtools RSQLite rstudioapi rtracklayer ruv S4Arrays S4Vectors sass scales scrime siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex TxDb.Hsapiens.UCSC.hg19.knownGene tzdb UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite vroom withr xfun XML xml2 xtable XVector yaml zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
DMR calling from bisulfite sequencing and Illumina array data	DMRcate-package DMRcate
Change the individual CpG FDR thresholding for a CpGannotated object.	changeFDR
Annotate Illumina CpGs with their chromosome position and test statistic	cpg.annotate
An object summarising individual CpG sites fitted to a given model	CpGannotated-class
Plotting DMRs	DMR.plot plot
DMR identification	dmrcate
Initial storage object for called DMRs - class	DMResults-class
Create a GRanges object from 'dmrcate' output.	extractRanges
Filter out position replicates from an EPICv2 beta- or M-matrix	rmPosReps
Filter probes	rmSNPandCH
Annotate a bisulfite sequencing experiment (WGBS or RRBS) with probe weights and chromosomal position.	sequencing.annotate

Package: DMRcate 3.1.4

DMRcate: Methylation array and sequencing spatial analysis methods

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