DMRcaller: Differentially Methylated Regions caller

Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is the CX report files produced by Bismark and the output is a list of DMRs stored as GRanges objects.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DMRcaller")
AuthorNicolae Radu Zabet <n.r.zabet@gen.cam.ac.uk> and Jonathan Michael Foonlan Tsang <jmft2@cam.ac.uk>
Bioconductor views Coverage DNAMethylation DifferentialMethylation Sequencing Software
Date of publicationNone
MaintainerNicolae Radu Zabet <n.r.zabet@gen.cam.ac.uk>
LicenseGPL-3
Version1.6.0

View on Bioconductor

Functions

analyseReadsInsideRegionsForCondition Man page
computeDMRs Man page
computeMethylationDataCoverage Man page
computeMethylationProfile Man page
computeOverlapProfile Man page
DMRcaller Man page
DMRcaller-package Man page
DMRsNoiseFilterCG Man page
filterDMRs Man page
GEs Man page
getWholeChromosomes Man page
mergeDMRsIteratively Man page
methylationDataList Man page
plotLocalMethylationProfile Man page
plotMethylationDataCoverage Man page
plotMethylationProfile Man page
plotMethylationProfileFromData Man page
plotOverlapProfile Man page
poolMethylationDatasets Man page
poolTwoMethylationDatasets Man page
readBismark Man page
readBismarkPool Man page
saveBismark Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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