Package: DMRcaller 1.39.0

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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DMRcaller.pdf |DMRcaller.html✨
DMRcaller/json (API)
NEWS

# Install 'DMRcaller' in R:
install.packages('DMRcaller', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

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.

differentialmethylationdnamethylationsoftwaresequencingcoverage

3.30 score 8 scripts 235 downloads 22 exports 28 dependencies

Last updated 23 days agofrom:13a82ad608. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:analyseReadsInsideRegionsForConditioncomputeDMRscomputeDMRsReplicatescomputeMethylationDataCoveragecomputeMethylationDataSpatialCorrelationcomputeMethylationProfilecomputeOverlapProfilefilterDMRsgetWholeChromosomesjoinReplicatesmergeDMRsIterativelyplotLocalMethylationProfileplotMethylationDataCoverageplotMethylationDataSpatialCorrelationplotMethylationProfileplotMethylationProfileFromDataplotOverlapProfilepoolMethylationDatasetspoolTwoMethylationDatasetsreadBismarkreadBismarkPoolsaveBismark

Dependencies:askpassbetaregBiocGenericscurlflexmixFormulaGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticelmtestmimemodeltoolsnnetopensslR6RcppRcppRollS4VectorssandwichsysUCSC.utilsXVectorzlibbioczoo

DMRcaller

Rendered fromDMRcaller.Rnwusingknitr::knitron Oct 30 2024.

Last update: 2018-07-16
Started: 2015-04-01

Readme and manuals

Help Manual

Help pageTopics
Analyse reads inside regions for conditionanalyseReadsInsideRegionsForCondition
Compute DMRscomputeDMRs
Compute DMRscomputeDMRsReplicates
Compute methylation data coveragecomputeMethylationDataCoverage
Compute methylation data spatial correlationcomputeMethylationDataSpatialCorrelation
Compute methylation profilecomputeMethylationProfile
Compute Overlaps ProfilecomputeOverlapProfile
Call Differentially Methylated Regions (DMRs) between two samplesDMRcaller-package DMRcaller
The DMRs between WT and met1-3 in CG contextDMRsNoiseFilterCG
Extract GCextractGC
Filter DMRsfilterDMRs
The genetic elements dataGEs
Get whole chromosomes from methylation datagetWholeChromosomes
Joins together two GRange objects in a single containing all the replicatesjoinReplicates
Merge DMRs iterativelymergeDMRsIteratively
The methylation data listmethylationDataList
Plot local methylation profileplotLocalMethylationProfile
Plot methylation data coverageplotMethylationDataCoverage
Plot methylation data spatial correlationplotMethylationDataSpatialCorrelation
Plot Methylation ProfileplotMethylationProfile
Plot methylation profile from dataplotMethylationProfileFromData
Plot overlap profileplotOverlapProfile
Pool methylation datapoolMethylationDatasets
Pool two methylation datasetspoolTwoMethylationDatasets
Read BismarkreadBismark
Read Bismark poolreadBismarkPool
Save BismarksaveBismark
Simulated data for biological replicatessyntheticDataReplicates