Package: DMRcaller 1.37.0

Nicolae Radu Zabet

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.

Authors:Nicolae Radu Zabet <[email protected]>, Jonathan Michael Foonlan Tsang <[email protected]>, Alessandro Pio Greco <[email protected]> and Ryan Merritt <[email protected]>

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Peer review:

On BioConductor:DMRcaller-1.37.0(bioc 3.20)DMRcaller-1.36.0(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

22 exports 2.09 score 28 dependencies 6 mentions

Last updated 2 months agofrom:72bb239a4d

Exports:analyseReadsInsideRegionsForConditioncomputeDMRscomputeDMRsReplicatescomputeMethylationDataCoveragecomputeMethylationDataSpatialCorrelationcomputeMethylationProfilecomputeOverlapProfilefilterDMRsgetWholeChromosomesjoinReplicatesmergeDMRsIterativelyplotLocalMethylationProfileplotMethylationDataCoverageplotMethylationDataSpatialCorrelationplotMethylationProfileplotMethylationProfileFromDataplotOverlapProfilepoolMethylationDatasetspoolTwoMethylationDatasetsreadBismarkreadBismarkPoolsaveBismark

Dependencies:askpassbetaregBiocGenericscurlflexmixFormulaGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticelmtestmimemodeltoolsnnetopensslR6RcppRcppRollS4VectorssandwichsysUCSC.utilsXVectorzlibbioczoo