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DMRcaller (version 1.4.2)

Differentially Methylated Regions caller

Description

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.

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Version

Version

1.4.2

License

GPL-3

Maintainer

Nicolae Radu Zabet

Last Published

February 15th, 2017

Functions in DMRcaller (1.4.2)

DMRsNoiseFilterCG

The DMRs between WT and met1-3 in CG context
computeMethylationDataCoverage

Compute methylation data coverage
plotMethylationDataCoverage

Plot methylation data coverage
readBismarkPool

Read Bismark pool
DMRcaller

Call Differentially Methylated Regions (DMRs) between two samples
plotMethylationProfile

Plot Methylation Profile
computeOverlapProfile

Compute Overlaps Profile
filterDMRs

Filter DMRs
mergeDMRsIteratively

Merge DMRs iteratively
poolMethylationDatasets

Pool methylation data
computeMethylationProfile

Compute methylation profile
plotLocalMethylationProfile

Plot local methylation profile
readBismark

Read Bismark
plotMethylationProfileFromData

Plot methylation profile from data
getWholeChromosomes

Get whole chromosomes from methylation data
computeDMRs

Compute DMRs
poolTwoMethylationDatasets

Pool two methylation datasets
saveBismark

Save Bismark
plotOverlapProfile

Plot overlap profile
analyseReadsInsideRegionsForCondition

Analyse reads inside regions for condition
methylationDataList

The methylation data list
GEs

The genetic elements data