{ "_id": "6ab8facf99f7aa8c6aa393ee", "Package": "DMRcaller", "Type": "Package", "Title": "Differentially Methylated Regions Caller", "Version": "1.45.3", "Date": "2019-01-18", "Encoding": "UTF-8", "Authors@R": "c(person(given=\"Nicolae Radu\", family=\"Zabet\", role =\nc(\"aut\",\"cre\"), email = \"r.zabet@qmul.ac.uk\"),\nperson(given=\"Jonathan\", family=\"Tsang\", role = \"aut\", email =\n\"jmft2@cam.ac.uk\"), person(given=\"Alessandro\", family=\"Greco\",\nrole = \"aut\", email = \"apgrec@essex.ac.uk\"), person(given=\"Ryan\",\nfamily=\"Merritt\", role = \"aut\", email = \"rmerri@essex.ac.uk\"), person(given=\"Young Jun\",\nfamily=\"Kim\", role = \"aut\", email = \"qc25039@qmul.ac.uk\"))", "Author": "Nicolae Radu Zabet , Jonathan Michael\nFoonlan Tsang , Alessandro Pio Greco\n, Ryan Merritt and\nYoung Jun Kim ", "Maintainer": "Nicolae Radu Zabet ", "Description": "Uses Bisulfite sequencing data in two conditions and\nidentifies differentially methylated regions between the\nconditions in CG and non-CG context. The input is the CX report\nfiles produced by Bismark and the output is a list of DMRs\nstored as GRanges objects.", "License": "GPL-3", "LazyLoad": "yes", "biocViews": "DifferentialMethylation, DNAMethylation, Software,\nSequencing, Coverage", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-07-27 16:46:23 UTC", "RemoteUrl": "https://github.com/bioc/DMRcaller", "RemoteRef": "HEAD", "RemoteSha": "cae718d93dbdaa5ce393ad7e0849ba7fbdd3c6c3", "Packaged": { "Date": "2026-09-27 11:02:30 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "DMRcaller_1.45.3.tar.gz", "_fileid": "https://r2.ropensci.org/b30b20c7be366fd4f9101be821551fb4e89a1e6e78996ed08fc4cf604d8a3f8e", "_filesize": 3826808, "_sha256": 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[], "table": false, "tojson": false }, { "name": "ont_gr_GM18870_chr1_sorted_bins_1k", "title": "The ONT methylation data example", "object": "ont_gr_GM18870_chr1_sorted_bins_1k", "file": "ont_gr_GM18870_chr1_sorted_bins_1k.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "ontSampleGRangesList", "title": "The ONT methylation data list", "object": "ontSampleGRangesList", "file": "ontSampleGRangesList.RData", "class": [ "CompressedGRangesList" ], "fields": [], "table": false, "tojson": false }, { "name": "PMDsBinsCG", "title": "The PMDs between GM18501 and GM18876 using Bins method", "object": "PMDsBinsCG", "file": "PMDsBinsCG.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "PMDsNoiseFilterCG", "title": "The PMDs between GM18501 and GM18876 using Noise_filter method", "object": "PMDsNoiseFilterCG", "file": "PMDsNoiseFilterCG.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "syntheticDataReplicates", "title": "Simulated data for biological replicates", "object": "syntheticDataReplicates", "file": "syntheticDataReplicates.RData", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "dot-analyseReadsInsideBins", "title": "Analyse reads inside regions", "topics": [ ".analyseReadsInsideBins" ] }, { "page": "dot-analyseReadsInsideBinsOneSample", "title": "Analyse reads inside regions for one sample", "topics": [ ".analyseReadsInsideBinsOneSample" ] }, { "page": "dot-analyseReadsInsideBinsPMDs", "title": "Analyse reads inside regions", "topics": [ ".analyseReadsInsideBinsPMDs" ] }, { "page": "dot-analyseReadsInsideBinsReplicates", "title": "Analyse reads inside regions", "topics": [ ".analyseReadsInsideBinsReplicates" ] }, { "page": "dot-analyseReadsInsideRegions", "title": "Analyse reads inside regions", "topics": [ ".analyseReadsInsideRegions" ] }, { "page": "dot-analyseReadsInsideRegionsForCondition", "title": "Analyse reads inside regions", "topics": [ ".analyseReadsInsideRegionsForCondition" ] }, { "page": "dot-analyseReadsInsideRegionsOneSample", "title": "Analyse reads inside regions", "topics": [ ".analyseReadsInsideRegionsOneSample" ] }, { "page": "dot-analyseReadsInsideRegionsPMDs", "title": "Analyse reads inside regions", "topics": [ ".analyseReadsInsideRegionsPMDs" ] }, { "page": "dot-analyseReadsInsideRegionsReplicates", "title": "Analyse reads inside regions", "topics": [ ".analyseReadsInsideRegionsReplicates" ] }, { "page": "dot-analyseReadsInsideRegionsVMDs", "title": "Analyse reads inside regions with computing mean and standard deviation per-read proportions", "topics": [ ".analyseReadsInsideRegionsVMDs" ] }, { "page": "dot-analyseReadsInsideRegionsVMR", "title": "Analyse reads inside regions (with VMR testing)", "topics": [ ".analyseReadsInsideRegionsVMR" ] }, { "page": "dot-computeaAjustedPValuesInDMRs", "title": "Compute adjusted p-values in DMRs", "topics": [ ".computeaAjustedPValuesInDMRs" ] }, { "page": "dot-computeaAjustedPValuesInDMRsReplicates", "title": "Compute adjusted p-values", "topics": [ ".computeaAjustedPValuesInDMRsReplicates" ] }, { "page": "dot-computeAdjuestedPValues", "title": "Compute adjusted p-values", "topics": [ ".computeAdjuestedPValues" ] }, { "page": "dot-computeAdjuestedPValuesReplicates", "title": "Compute adjusted p-values", "topics": [ ".computeAdjuestedPValuesReplicates" ] }, { "page": "dot-computeBetaReg", "title": "This function applies the .computeBetaRegSingle to the entire dataset", "topics": [ ".computeBetaReg" ] }, { "page": "dot-computeBetaRegSingle", "title": "Beta regression", "topics": [ ".computeBetaRegSingle" ] }, { "page": "dot-computeDMRsBins", "title": "This function computes the differentially methylated regions between two conditions using the bins method.", "topics": [ ".computeDMRsBins" ] }, { "page": "dot-computeDMRsNeighbourhood", "title": "This function computes the differentially methylated regions between two conditions using the neighbourhood method. This assumes the computation of differentially methylated cytosines followed by smart merging of these cytosines while keeping the new DMRs statistically significant.", "topics": [ ".computeDMRsNeighbourhood" ] }, { "page": "dot-computeDMRsNoiseFilter", "title": "This function computes the differentially methylated regions between two conditions using the noise filter method.", "topics": [ ".computeDMRsNoiseFilter" ] }, { "page": "dot-computeDMRsReplicatesBins", "title": "This function computes the differentially methylated regions between replicates using the bins method.", "topics": [ ".computeDMRsReplicatesBins" ] }, { "page": "dot-computeDMRsReplicatesNeighbourhood", "title": "This function computes the differentially methylated regions between replicates using the neighbourhood method.", "topics": [ ".computeDMRsReplicatesNeighbourhood" ] }, { "page": "dot-computeMethylationDataSpatialCorrelation", "title": "Compute methylation data spatial correlation", "topics": [ ".computeMethylationDataSpatialCorrelation" ] }, { "page": "dot-computePMDsBins", "title": "This function computes the partially methylated regions using the bins method.", "topics": [ ".computePMDsBins" ] }, { "page": "dot-computePMDsNeighbourhood", "title": "This function computes the partially methylated domains using the neighbourhood method. This assumes the computation of partially methylated cytosines followed by smart merging of these cytosines while keeping the new PMDs statistically significant.", "topics": [ ".computePMDsNeighbourhood" ] }, { "page": "dot-computePMDsNoiseFilter", "title": "This function computes the partially methylated regions using the noise filter method.", "topics": [ ".computePMDsNoiseFilter" ] }, { "page": "dot-computeProportionsInDMRs", "title": "This function recalculate proportions between methylated and total reads in a new region.", "topics": [ ".computeProportionsInDMRs" ] }, { "page": "dot-computeVMDsBins", "title": "This function computes the variance methylated regions using the bins method.", "topics": [ ".computeVMDsBins" ] }, { "page": "dot-convertResult", "title": "This function extracts the p-value for each cytosine from the betareg object", "topics": [ ".convertResult" ] }, { "page": "dot-countCytosinesInside", "title": "Count cytosines inside", "topics": [ ".countCytosinesInside" ] }, { "page": "dot-countMethylationDataCoverage", "title": "Count methylation data coverage", "topics": [ ".countMethylationDataCoverage" ] }, { "page": "dot-countTotalNumberOfCytosines", "title": "Count total number of Cytosines", "topics": [ ".countTotalNumberOfCytosines" ] }, { "page": "dot-fisherTest", "title": "Fisher test", "topics": [ ".fisherTest" ] }, { "page": "dot-fisherTestPValue", "title": "Fisher test", "topics": [ ".fisherTestPValue" ] }, { "page": "dot-isColor", "title": "Is color", "topics": [ ".isColor" ] }, { "page": "dot-isInteger", "title": ".is.integer", "topics": [ ".isInteger" ] }, { "page": "dot-joinMethylationData", "title": "Join methylation data", "topics": [ ".joinMethylationData" ] }, { "page": "dot-mergeDMRsIteratively", "title": "This takes a list of DMRs and attempts to merge DMRs while keeping the new DMRs statistically significant", "topics": [ ".mergeDMRsIteratively" ] }, { "page": "dot-mergePMDsIteratively", "title": "This takes a list of PMDs and attempts to merge PMDs while keeping the new PMDs filtering by the preset parameter", "topics": [ ".mergePMDsIteratively" ] }, { "page": "dot-movingAverage", "title": "Moving average", "topics": [ ".movingAverage" ] }, { "page": "dot-movingSum", "title": "Moving sum", "topics": [ ".movingSum" ] }, { "page": "dot-plotGeneticElements", "title": "Plot genetic elements", "topics": [ ".plotGeneticElements" ] }, { "page": "dot-printGenomicRanges", "title": "Print GenomicRanges", "topics": [ ".printGenomicRanges" ] }, { "page": "dot-scoreTest", "title": "Score test", "topics": [ ".scoreTest" ] }, { "page": "dot-smartMergeDMRs", "title": "This takes a list of DMRs and attempts to merge DMRs while keeping the new DMRs statistically significant", "topics": [ ".smartMergeDMRs" ] }, { "page": "dot-smartMergeDMRsReplicates", "title": "This takes a list of DMRs and attempts to merge DMRs while keeping the new DMRs statistically significant", "topics": [ ".smartMergeDMRsReplicates" ] }, { "page": "dot-smartMergePMDs", "title": "This takes a list of PMDs and attempts to merge PMDs while keeping the new PMDs statistically significant", "topics": [ ".smartMergePMDs" ] }, { "page": "dot-splitGRangesEqualy", "title": ".splitGRangesEqualy", "topics": [ ".splitGRangesEqualy" ] }, { "page": "dot-stopIfNotAll", "title": ".stopIfNotAll", "topics": [ ".stopIfNotAll" ] }, { "page": "dot-validateConditionReplicates", "title": "Validate the condition of the experiment", "topics": [ ".validateConditionReplicates" ] }, { "page": "dot-validateGRanges", "title": "Validate GRanges", "topics": [ ".validateGRanges" ] }, { "page": "dot-validateMethylationData", "title": "Validate methylation data", "topics": [ ".validateMethylationData" ] }, { "page": "dot-validateMethylationDataList", "title": "Validate methylation data", "topics": [ ".validateMethylationDataList" ] }, { "page": "dot-validateMethylationProfile", "title": "Validate methylation profile", "topics": [ ".validateMethylationProfile" ] }, { "page": "dot-validateModif", "title": "Validate Modification Tag in BAM", "topics": [ ".validateModif" ] }, { "page": "dot-validateStatisticalTest", "title": "Validate statistial test", "topics": [ ".validateStatisticalTest" ] }, { "page": "dot-validateStatisticalTestReplicates", "title": "Validate statistial test", "topics": [ ".validateStatisticalTestReplicates" ] }, { "page": "analyseReadsInsideRegionsForCondition", "title": "Analyse reads inside regions for condition", "topics": [ "analyseReadsInsideRegionsForCondition" ] }, { "page": "analyseReadsInsideRegionsForConditionPMD", "title": "Analyse reads inside regions for condition", "topics": [ "analyseReadsInsideRegionsForConditionPMD" ] }, { "page": "computeCoMethylatedPositions", "title": "Compute pairwise co-methylation statistics for cytosine sites within regions", "topics": [ "computeCoMethylatedPositions" ] }, { "page": "computeCoMethylatedRegions", "title": "Compute pairwise co-methylation statistics between regions", "topics": [ "computeCoMethylatedRegions" ] }, { "page": "computeDMRs", "title": "Compute DMRs", "topics": [ "computeDMRs" ] }, { "page": "computeDMRsReplicates", "title": "Compute DMRs", "topics": [ "computeDMRsReplicates" ] }, { "page": "computeMethylationDataCoverage", "title": "Compute methylation data coverage", "topics": [ "computeMethylationDataCoverage" ] }, { "page": "computeMethylationDataSpatialCorrelation", "title": "Compute methylation data spatial correlation", "topics": [ "computeMethylationDataSpatialCorrelation" ] }, { "page": "computeMethylationProfile", "title": "Compute methylation profile", "topics": [ "computeMethylationProfile" ] }, { "page": "computeOverlapProfile", "title": "Compute Overlaps Profile", "topics": [ "computeOverlapProfile" ] }, { "page": "computePMDs", "title": "Compute PMDs", "topics": [ "computePMDs" ] }, { "page": "computeVMDs", "title": "Compute VMDs", "topics": [ "computeVMDs" ] }, { "page": "DMRcaller", "title": "Call Differentially Methylated Regions (DMRs) between two samples", "topics": [ "DMRcaller-package", "DMRcaller" ] }, { "page": "DMRsNoiseFilterCG", "title": "The DMRs between WT and met1-3 in CG context", "topics": [ "DMRsNoiseFilterCG" ] }, { "page": "extractGC", "title": "Extract GC", "topics": [ "extractGC" ] }, { "page": "filterDMRs", "title": "Filter DMRs", "topics": [ "filterDMRs" ] }, { "page": "filterPMDs", "title": "Filter PMDs", "topics": [ "filterPMDs" ] }, { "page": "filterVMDs", "title": "Filter VMDs", "topics": [ "filterVMDs" ] }, { "page": "filterVMRsONT", "title": "Filter VMRs for ONT Data", "topics": [ "filterVMRsONT" ] }, { "page": "GEs", "title": "The genetic elements data", "topics": [ "GEs" ] }, { "page": "GEs_hg38", "title": "The genetic elements data of GRCh38 Genome Reference", "topics": [ "GEs_hg38" ] }, { "page": "getWholeChromosomes", "title": "Get whole chromosomes from methylation data", "topics": [ "getWholeChromosomes" ] }, { "page": "joinReplicates", "title": "Joins together two GRange objects in a single containing all the replicates", "topics": [ "joinReplicates" ] }, { "page": "mergeDMRsIteratively", "title": "Merge DMRs iteratively", "topics": [ "mergeDMRsIteratively" ] }, { "page": "mergePMDsIteratively", "title": "Merge PMDs iteratively", "topics": [ "mergePMDsIteratively" ] }, { "page": "methylationDataList", "title": "The methylation data list", "topics": [ "methylationDataList" ] }, { "page": "ont_gr_GM18870_chr1_PMD_bins_1k", "title": "Partially Methilated Domains example", "topics": [ "ont_gr_GM18870_chr1_PMD_bins_1k" ] }, { "page": "ont_gr_GM18870_chr1_sorted_bins_1k", "title": "The ONT methylation data example", "topics": [ "ont_gr_GM18870_chr1_sorted_bins_1k" ] }, { "page": "ontSampleGRangesList", "title": "The ONT methylation data list", "topics": [ "ontSampleGRangesList" ] }, { "page": "plotLocalMethylationProfile", "title": "Plot local methylation profile", "topics": [ "plotLocalMethylationProfile" ] }, { "page": "plotMethylationDataCoverage", "title": "Plot methylation data coverage", "topics": [ "plotMethylationDataCoverage" ] }, { "page": "plotMethylationDataSpatialCorrelation", "title": "Plot methylation data spatial correlation", "topics": [ "plotMethylationDataSpatialCorrelation" ] }, { "page": "plotMethylationProfile", "title": "Plot Methylation Profile", "topics": [ "plotMethylationProfile" ] }, { "page": "plotMethylationProfileFromData", "title": "Plot methylation profile from data", "topics": [ "plotMethylationProfileFromData" ] }, { "page": "plotOverlapProfile", "title": "Plot overlap profile", "topics": [ "plotOverlapProfile" ] }, { "page": "PMDsBinsCG", "title": "The PMDs between GM18501 and GM18876 using Bins method", "topics": [ "PMDsBinsCG" ] }, { "page": "PMDsNoiseFilterCG", "title": "The PMDs between GM18501 and GM18876 using Noise_filter method", "topics": [ "PMDsNoiseFilterCG" ] }, { "page": "poolMethylationDatasets", "title": 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\\texttt{r.zabet@qmul.ac.uk}, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK}", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2025-09-03 16:29:10", "modified": "2025-10-17 13:51:50", "commits": 5 } ], "_score": 5.760422483423213, "_indexed": true, "_nocasepkg": "dmrcaller", "_universes": [ "bioc", "nrzabet" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.45.3", "date": "2026-09-27T11:06:57.000Z", "distro": "resolute", "commit": "cae718d93dbdaa5ce393ad7e0849ba7fbdd3c6c3", "fileid": "https://r2.ropensci.org/aaf511318d3b954cb578d308dbd4b3044a6043a03439c34a13d3d37280d285a8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36314168107" }, { "r": "4.6.1", "os": "linux", "version": "1.45.3", "date": "2026-09-27T11:08:00.000Z", "distro": "resolute", "commit": "cae718d93dbdaa5ce393ad7e0849ba7fbdd3c6c3", "fileid": "https://r2.ropensci.org/8f1f33d23a0559cbd8a2491efe39d69364f0684f9d055ce793d08e639e061704", "status": "success", "check": "WARNING", "buildurl": 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