DMRcate: Methylation array and sequencing spatial analysis methods

Share:

De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulphite 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.

Author
Tim Peters
Date of publication
None
Maintainer
Tim Peters <t.peters@garvan.org.au>
License
file LICENSE
Version
1.10.1

View on Bioconductor

Man pages

cpg.annotate
Annotate CpGs with their chromosome position and test...
dmrcate
DMR identification
DMRcate-internal
Internal DMRcate objects and functions
DMRcate-package
DMR calling from bisulphite sequencing and Illumina array...
DMR.plot
Plotting DMRs
extractRanges
Create GRanges object from 'dmrcate' output.
rmSNPandCH
Filter probes

Files in this package

DMRcate/DESCRIPTION
DMRcate/LICENSE
DMRcate/NAMESPACE
DMRcate/NEWS
DMRcate/R
DMRcate/R/DMR.plot.R
DMRcate/R/KernelSums.R
DMRcate/R/KernelTest.R
DMRcate/R/SparseDeltas.R
DMRcate/R/cpg.annotate.R
DMRcate/R/dmrcate.R
DMRcate/R/extractCoords.R
DMRcate/R/extractRanges.R
DMRcate/R/fitParallel.R
DMRcate/R/rmSNPandCH.R
DMRcate/build
DMRcate/build/vignette.rds
DMRcate/data
DMRcate/inst
DMRcate/inst/CITATION
DMRcate/inst/doc
DMRcate/inst/doc/DMRcate.R
DMRcate/inst/doc/DMRcate.Rnw
DMRcate/inst/doc/DMRcate.pdf
DMRcate/inst/unitTests
DMRcate/inst/unitTests/test_pipeline.R
DMRcate/man
DMRcate/man/DMR.plot.Rd
DMRcate/man/DMRcate-internal.Rd
DMRcate/man/DMRcate-package.Rd
DMRcate/man/cpg.annotate.Rd
DMRcate/man/dmrcate.Rd
DMRcate/man/extractRanges.Rd
DMRcate/man/rmSNPandCH.Rd
DMRcate/tests
DMRcate/tests/runTests.R
DMRcate/vignettes
DMRcate/vignettes/DMRcate.Rnw
DMRcate/vignettes/heynSNP.pdf