Introduction | Methods | Description | Data | Bisulfite sequencing data | Oxford Nanopore methylation data | Oxford Nanopore cytosine reference selection | Reading Oxford Nanopore BAM files | Low resolution profiles | Coverage of the bisulfite sequencing data | Spatial correlation of methylation levels | Calling DMRs | Merge DMRs | Calling DMRs using biological replicates | Extract methylation data in regions | Calling partially methylated domains (PMDs) | Calling variably methylated domains (VMDs) using ONT data | Detecting Variably Methylated Regions (VMRs) using ONT data | Calling Co-Methylated Positions (CMPs) using ONT data | Calling Co-Methylated Regions (CMRs) using ONT Data | Plotting the distribution of DMRs, PMDs, VMDs or VMRs | Plotting profiles with DMRs, PMDs, VMDs or VMRs | Parallel computation | Session information | References
Package: DMRcaller 1.45.1
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:
DMRcaller_1.45.1.tar.gz
DMRcaller_1.45.1.zip(r-4.7)DMRcaller_1.45.1.zip(r-4.6)DMRcaller_1.45.1.zip(r-4.5)
DMRcaller_1.45.1.tgz(r-4.6-any)DMRcaller_1.45.1.tgz(r-4.5-any)
DMRcaller_1.45.1.tar.gz(r-4.7-any)DMRcaller_1.45.1.tar.gz(r-4.6-any)
DMRcaller_1.45.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DMRcaller/json (API)
| # Install 'DMRcaller' in R: |
| install.packages('DMRcaller', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- DMRsNoiseFilterCG - The DMRs between WT and met1-3 in CG context
- GEs - The genetic elements data
- GEs_hg38 - The genetic elements data of GRCh38 Genome Reference
- methylationDataList - The methylation data list
- ont_gr_GM18870_chr1_PMD_bins_1k - Partially Methilated Domains example
- ont_gr_GM18870_chr1_sorted_bins_1k - The ONT methylation data example
- ontSampleGRangesList - The ONT methylation data list
- PMDsBinsCG - The PMDs between GM18501 and GM18876 using Bins method
- PMDsNoiseFilterCG - The PMDs between GM18501 and GM18876 using Noise_filter method
- syntheticDataReplicates - Simulated data for biological replicates
On BioConductor:DMRcaller-1.45.0(bioc 3.24)DMRcaller-1.44.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
differentialmethylationdnamethylationsoftwaresequencingcoverage
Last updated from:17147d6901. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 272 | ||
| linux-devel-x86_64 | ERROR | 623 | ||
| source / vignettes | OK | 432 | ||
| linux-release-x86_64 | ERROR | 620 | ||
| macos-release-arm64 | ERROR | 534 | ||
| macos-oldrel-arm64 | ERROR | 354 | ||
| windows-devel | ERROR | 518 | ||
| windows-release | ERROR | 614 | ||
| windows-oldrel | ERROR | 538 | ||
| wasm-release | OK | 212 |
Exports:analyseReadsInsideRegionsForConditionanalyseReadsInsideRegionsForConditionPMDcomputeCoMethylatedPositionscomputeCoMethylatedRegionscomputeDMRscomputeDMRsReplicatescomputeMethylationDataCoveragecomputeMethylationDataSpatialCorrelationcomputeMethylationProfilecomputeOverlapProfilecomputePMDscomputeVMDsfilterDMRsfilterPMDsfilterVMDsfilterVMRsONTgetWholeChromosomesjoinReplicatesmergeDMRsIterativelymergePMDsIterativelyplotLocalMethylationProfileplotMethylationDataCoverageplotMethylationDataSpatialCorrelationplotMethylationProfileplotMethylationProfileFromDataplotOverlapProfilepoolMethylationDatasetspoolTwoMethylationDatasetsreadBismarkreadBismarkPoolreadONTbamsaveBismarkselectCytosine
Dependencies:abindaskpassbetaregBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitopsBSgenomecigarilloclicodetoolscpp11crayoncurlDelayedArrayflexmixformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesgluehttrinflectionInteractionSetIRangesjsonlitelambda.rlatticelifecyclelmtestmagrittrMatrixMatrixGenericsmatrixStatsmimemodeltoolsnnetopensslR6RcppRcppRollRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssandwichSeqinfosnowSparseArraystringistringrSummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzoo
