{
  "_id": "6a623ce735834fefe99ecc68",
  "Package": "mesa",
  "Title": "Methylation Enrichment Sequencing Analysis",
  "Version": "0.99.5",
  "Authors@R": "c(\nperson(given = \"Simon\",\nfamily = \"Pearce\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0002-1680-5538\")),\nperson(given = \"Steven\",\nfamily = \"Hill\",\nrole = c(\"aut\", \"cre\"),\nemail = \"stevenhill.work@gmail.com\",\ncomment = c(ORCID = \"0000-0002-5909-692X\")),\nperson(given = \"Paddy\",\nfamily = \"Harker\",\nrole = \"ctb\",\ncomment = c(ORCID = \"0000-0002-2531-8774\")),\nperson(given = \"Kevin\",\nfamily = \"Brennan\",\nrole = \"ctb\",\nemail = \"kevin.brennan@cruk.manchester.ac.uk\",\ncomment = c(ORCID = \"0000-0001-9018-9852\")),\nperson(given = \"Katarzyna\",\nfamily = \"Kamieniecka\",\nrole = \"ctb\"),\nperson(given = \"Felipe\",\nfamily = \"Perez Martinez\",\nrole = \"ctb\",\nemail = \"felipe.perezmartinez@cruk.manchester.ac.uk\",\ncomment = c(ORCID = \"0009-0007-9138-3674\")),\nperson(given = \"Cancer Research UK National Biomarker Centre\",\nrole = c(\"cph\", \"fnd\"))\n)",
  "Description": "A package for the analysis of methylation enrichment\nsequencing data (e.g. MBD-seq or MEDIP-seq). This allows for\nthe window-based evaluation of methylation levels (using the\n'qsea' package), including functions for determining\ndifferentially methylated regions. Many functions are provided\nfor tidyverse style modification of the qseaSet objects\noriginally defined in 'qsea'.",
  "License": "GPL (>=2)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "LazyDataCompression": "xz",
  "Roxygen": "list(markdown = TRUE)",
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  "VignetteBuilder": "knitr",
  "biocViews": "Sequencing, DNAMethylation, CpGIsland, Preprocessing,\nNormalization, QualityControl, Visualization,\nCopyNumberVariation, DifferentialMethylation, Coverage,\nChIPSeq, ChipOnChip",
  "Config/testthat/edition": "3",
  "URL": "https://github.com/cruk-mi/mesa",
  "BugReports": "https://github.com/cruk-mi/mesa",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev perl\nlibx11-dev xz-utils zlib1g-dev",
  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-06-26 10:57:27 UTC",
  "RemoteUrl": "https://github.com/BiocStaging/mesa",
  "RemoteRef": "HEAD",
  "RemoteSha": "61c890a5836b061eb9bd1b3f077d24768faa1469",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-23 15:54:15 UTC",
    "User": "root"
  },
  "Author": "Simon Pearce [aut] (ORCID: <https://orcid.org/0000-0002-1680-5538>),\nSteven Hill [aut, cre] (ORCID: <https://orcid.org/0000-0002-5909-692X>),\nPaddy Harker [ctb] (ORCID: <https://orcid.org/0000-0002-2531-8774>),\nKevin Brennan [ctb] (ORCID: <https://orcid.org/0000-0001-9018-9852>),\nKatarzyna Kamieniecka [ctb],\nFelipe Perez Martinez [ctb] (ORCID:\n<https://orcid.org/0009-0007-9138-3674>),\nCancer Research UK National Biomarker Centre [cph, fnd]",
  "Maintainer": "Steven Hill <stevenhill.work@gmail.com>",
  "_user": "biocstaging",
  "_type": "src",
  "_file": "mesa_0.99.5.tar.gz",
  "_fileid": "https://r2.ropensci.org/afb9535214db663cab7459c2187da7984f1f972837e331b6a8c3fe4cf3b79ed0",
  "_filesize": 5322517,
  "_sha256": "afb9535214db663cab7459c2187da7984f1f972837e331b6a8c3fe4cf3b79ed0",
  "_expires": "2026-10-31T16:10:12.000Z",
  "_created": "2026-07-23T15:54:15.000Z",
  "_published": "2026-07-23T16:10:15.243Z",
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 5
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  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/30021734088",
  "_status": "failure",
  "_upstream": "https://github.com/BiocStaging/mesa",
  "_commit": {
    "id": "61c890a5836b061eb9bd1b3f077d24768faa1469",
    "author": "Felipe <92517493+fpmartinez10@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "chore(version): bump to 0.99.5 (#94)\n\nBump DESCRIPTION Version and rename the NEWS.md devel heading from\n0.99.4.9000 to the 0.99.5 release, mirroring PR #86.\n\nCo-authored-by: Claude <noreply@anthropic.com>",
    "time": 1782471447
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    "login": "steven-m-hill",
    "description": "Bioinformatician/Biostatistician at Cancer Research UK National Biomarker Centre, University of Manchester",
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      ],
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      "table": true,
      "tojson": true
    },
    {
      "name": "map_hg38_500kb",
      "title": "Mappability across the human genome (hg38/GRCh38)",
      "object": "map_hg38_500kb",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "chr",
        "start",
        "end",
        "map"
      ],
      "rows": 6188,
      "table": true,
      "tojson": true
    },
    {
      "name": "map_hg38_50kb",
      "title": "Mappability across the human genome (hg38/GRCh38)",
      "object": "map_hg38_50kb",
      "class": [
        "data.table",
        "data.frame"
      ],
      "fields": [
        "chr",
        "start",
        "end",
        "map"
      ],
      "rows": 61775,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "addBamCoveragePairedAndUnpaired",
      "title": "Add coverage to a qseaSet using proper pairs and/or high-quality R1 reads",
      "concept": [
        "coverage"
      ],
      "topics": [
        "addBamCoveragePairedAndUnpaired"
      ]
    },
    {
      "page": "addHMMcopyCNV",
      "title": "Add per-sample CNV calls to a qseaSet using HMMcopy",
      "concept": [
        "CNV"
      ],
      "topics": [
        "addHMMcopyCNV"
      ]
    },
    {
      "page": "addHyperStableFraction",
      "title": "Summarise the fraction of hyper-stable methylated regions (GRCh38 only)",
      "topics": [
        "addHyperStableFraction"
      ]
    },
    {
      "page": "addLibraryInformation",
      "title": "Add library metrics to the qseaSet sample table",
      "topics": [
        "addLibraryInformation"
      ]
    },
    {
      "page": "addMedipsEnrichmentFactors",
      "title": "Add MEDIPS-style enrichment metrics to a qseaSet sample table",
      "topics": [
        "addMedipsEnrichmentFactors"
      ]
    },
    {
      "page": "addNormalisation",
      "title": "Add qsea normalisation steps with defaults",
      "topics": [
        "addNormalisation"
      ]
    },
    {
      "page": "addSummaryAcrossWindows",
      "title": "Append window summaries to the sample table",
      "concept": [
        "window-summaries"
      ],
      "topics": [
        "addSummaryAcrossWindows"
      ]
    },
    {
      "page": "annotateWindows",
      "title": "Annotate genomic windows using ChIPseeker (with optional CpG/FANTOM context)",
      "topics": [
        "annotateWindows"
      ]
    },
    {
      "page": "arrange.qseaSet",
      "title": "Arrange (reorder) samples in a qseaSet via dplyr syntax",
      "topics": [
        "arrange.qseaSet"
      ]
    },
    {
      "page": "asValidGranges",
      "title": "Coerce common tabular inputs to GRanges",
      "topics": [
        "asValidGranges"
      ]
    },
    {
      "page": "BSgenome.CpG.distribution",
      "title": "Pre-calculated CpG distribution values for BSgenomes",
      "topics": [
        "BSgenome.Hsapiens.NCBI.GRCh38.CpG.distribution",
        "BSgenome.Hsapiens.UCSC.hg19.CpG.distribution",
        "BSgenome.Mmusculus.UCSC.mm10.CpG.distribution"
      ]
    },
    {
      "page": "calculateCGEnrichment",
      "title": "CpG enrichment from a BAM file (MEDIPS-style)",
      "topics": [
        "calculateCGEnrichment"
      ]
    },
    {
      "page": "calculateCGEnrichmentGRanges",
      "title": "CpG enrichment from GRanges of reads (MEDIPS-style)",
      "topics": [
        "calculateCGEnrichmentGRanges"
      ]
    },
    {
      "page": "calculateDMRs",
      "title": "Fit GLM and return DMR data in one step",
      "concept": [
        "DMR-detection"
      ],
      "topics": [
        "calculateDMRs"
      ]
    },
    {
      "page": "calculateFractionReadsInGRanges",
      "title": "Fraction of thresholded windows overlapping a set of regions",
      "concept": [
        "window-helpers"
      ],
      "topics": [
        "calculateFractionReadsInGRanges"
      ]
    },
    {
      "page": "calculateGenomicCGDistribution",
      "title": "Genome-wide CpG statistics (relH and GoGe)",
      "topics": [
        "calculateGenomicCGDistribution"
      ]
    },
    {
      "page": "colnames-qseaSet-method",
      "title": "Column names of a qseaSet sample table",
      "topics": [
        "colnames,qseaSet-method"
      ]
    },
    {
      "page": "combineQsets",
      "title": "Combine two qseaSets",
      "topics": [
        "combineQsets"
      ]
    },
    {
      "page": "combineQsetsList",
      "title": "Combine multiple qseaSets",
      "topics": [
        "combineQsetsList"
      ]
    },
    {
      "page": "convertToArrayBetaTable",
      "title": "Convert qsea beta values to array-like probe matrix",
      "concept": [
        "window-helpers"
      ],
      "topics": [
        "convertToArrayBetaTable"
      ]
    },
    {
      "page": "countWindowsAboveCutoff",
      "title": "Count windows above a cutoff",
      "concept": [
        "window-summaries"
      ],
      "topics": [
        "countWindowsAboveCutoff"
      ]
    },
    {
      "page": "downSample",
      "title": "Downsample reads in a qseaSet",
      "concept": [
        "window-helpers"
      ],
      "topics": [
        "downSample"
      ]
    },
    {
      "page": "ENCODEbadRegions",
      "title": "2019 ENCODE list of poorly mapped regions in hg38",
      "topics": [
        "ENCODEbadRegions"
      ]
    },
    {
      "page": "exampleMouse",
      "title": "A small example qseaSet with 5 paired tumour/normal samples.",
      "topics": [
        "exampleMouse"
      ]
    },
    {
      "page": "exampleTumourNormal",
      "title": "A small example qseaSet with 5 paired tumour/normal samples.",
      "topics": [
        "exampleTumourNormal"
      ]
    },
    {
      "page": "FantomRegions",
      "title": "FANTOM5 regions for GRCh38",
      "topics": [
        "FantomRegions"
      ]
    },
    {
      "page": "filter.qseaSet",
      "title": "Filter samples in a qseaSet",
      "topics": [
        "filter.qseaSet"
      ]
    },
    {
      "page": "alterQsetOverlap",
      "title": "Subset a qseaSet by overlaps / non-overlaps with genomic regions",
      "topics": [
        "filterByNonOverlaps",
        "filterByOverlaps"
      ]
    },
    {
      "page": "filterWindows",
      "title": "Filter regions (windows) inside a qseaSet",
      "topics": [
        "filterWindows"
      ]
    },
    {
      "page": "fitQseaGLM",
      "title": "Fit a generalized linear model (GLM) to a qseaSet",
      "concept": [
        "DMR-detection"
      ],
      "topics": [
        "fitQseaGLM"
      ]
    },
    {
      "page": "gc_hg38_1000kb",
      "title": "GC content across the human genome (hg38/GRCh38)",
      "topics": [
        "gc_hg38_1000kb",
        "gc_hg38_500kb",
        "gc_hg38_50kb"
      ]
    },
    {
      "page": "getBetaTable",
      "title": "Get beta per window",
      "concept": [
        "table-helpers"
      ],
      "topics": [
        "getBetaTable"
      ]
    },
    {
      "page": "getCGPositions",
      "title": "Genomic positions of a motif (CG) from MEDIPS",
      "topics": [
        "getCGPositions"
      ]
    },
    {
      "page": "getCountTable",
      "title": "Get counts per window",
      "concept": [
        "table-helpers"
      ],
      "topics": [
        "getCountTable"
      ]
    },
    {
      "page": "getDataTable",
      "title": "Extract per-window data (counts / NRPM / beta)",
      "concept": [
        "table-helpers"
      ],
      "topics": [
        "getDataTable"
      ]
    },
    {
      "page": "getDMRsData",
      "title": "Extract DMR-level results from a fitted GLM",
      "concept": [
        "DMR-detection"
      ],
      "topics": [
        "getDMRsData"
      ]
    },
    {
      "page": "getGenomicFeatureDistribution",
      "title": "Summarise signal by genomic context",
      "concept": [
        "annotation-summaries"
      ],
      "topics": [
        "getGenomicFeatureDistribution"
      ]
    },
    {
      "page": "getMesaAnnoDb",
      "title": "Get annotation DB for current or specified genome",
      "topics": [
        "getMesaAnnoDb"
      ]
    },
    {
      "page": "getMesaGenome",
      "title": "Get current mesa genome setting",
      "topics": [
        "getMesaGenome"
      ]
    },
    {
      "page": "getMesaTxDb",
      "title": "Get TxDb for current or specified genome",
      "topics": [
        "getMesaTxDb"
      ]
    },
    {
      "page": "getNRPMTable",
      "title": "Get NRPM per window",
      "concept": [
        "table-helpers"
      ],
      "topics": [
        "getNRPMTable"
      ]
    },
    {
      "page": "getPattern",
      "title": "Infer pattern names from region density columns",
      "topics": [
        "getPattern"
      ]
    },
    {
      "page": "getDimRed",
      "title": "Generate a PCA from a qseaSet",
      "concept": [
        "dimred-helpers"
      ],
      "topics": [
        "getDimRed",
        "getPCA",
        "getUMAP"
      ]
    },
    {
      "page": "getSampleQCSummary",
      "title": "Summarise key QC fields per sample",
      "topics": [
        "getSampleQCSummary"
      ]
    },
    {
      "page": "getWindowNames",
      "title": "Get window names from a qseaSet or ranges/table",
      "topics": [
        "getWindowNames"
      ]
    },
    {
      "page": "getWindows",
      "title": "Extract the regions (windows) used in a qseaSet",
      "topics": [
        "getWindows"
      ]
    },
    {
      "page": "hg19ToHg38.over.chain",
      "title": "hg19tohg38 liftover chain",
      "topics": [
        "hg19ToHg38.over.chain"
      ]
    },
    {
      "page": "hg38_450kArrayGR",
      "title": "Infinium 450k probe locations for hg38.",
      "topics": [
        "hg38_450kArrayGR"
      ]
    },
    {
      "page": "hg38CpGIslands",
      "title": "CpG islands for hg38.",
      "topics": [
        "hg38CpGIslands"
      ]
    },
    {
      "page": "hg38UltraStableProbes",
      "title": "Ultra-stable methylated regions (GRCh38)",
      "topics": [
        "hg38UltraStableProbes"
      ]
    },
    {
      "page": "is.qseaSet",
      "title": "Check whether an object is a qseaSet",
      "topics": [
        "is.qseaSet"
      ]
    },
    {
      "page": "left_join.mesaDimRed",
      "title": "Left-join onto the sample table of a mesaDimRed",
      "topics": [
        "left_join.mesaDimRed"
      ]
    },
    {
      "page": "left_join.qseaSet",
      "title": "Left join data onto a qseaSet sample table",
      "topics": [
        "left_join.qseaSet"
      ]
    },
    {
      "page": "liftOverHg19",
      "title": "Lift over genomic ranges from hg19 to hg38",
      "topics": [
        "liftOverHg19"
      ]
    },
    {
      "page": "makeAllContrasts",
      "title": "Generate all possible pairwise contrasts",
      "concept": [
        "DMR-detection"
      ],
      "topics": [
        "makeAllContrasts"
      ]
    },
    {
      "page": "makeQset",
      "title": "Construct an initial qseaSet from BAMs and metadata",
      "topics": [
        "makeQset"
      ]
    },
    {
      "page": "makeTransposedTable",
      "title": "Make a wide sample-by-window table",
      "concept": [
        "table-helpers"
      ],
      "topics": [
        "makeTransposedTable"
      ]
    },
    {
      "page": "map_hg38_1000kb",
      "title": "Mappability across the human genome (hg38/GRCh38)",
      "topics": [
        "map_hg38_1000kb",
        "map_hg38_500kb",
        "map_hg38_50kb"
      ]
    },
    {
      "page": "mesaDimRed-class",
      "title": "Dimensionality reduction results container",
      "topics": [
        "mesaDimRed",
        "mesaDimRed-class",
        "show,mesaDimRed-method"
      ]
    },
    {
      "page": "mesaPCA-class",
      "title": "PCA results container",
      "topics": [
        "mesaPCA",
        "mesaPCA-class",
        "show,mesaPCA-method"
      ]
    },
    {
      "page": "mesaUMAP-class",
      "title": "UMAP results container",
      "topics": [
        "mesaUMAP",
        "mesaUMAP-class",
        "show,mesaUMAP-method"
      ]
    },
    {
      "page": "mixSamples",
      "title": "Mix two samples to generate a synthetic qseaSet sample",
      "concept": [
        "sample-simulation"
      ],
      "topics": [
        "mixSamples"
      ]
    },
    {
      "page": "mutate.mesaDimRed",
      "title": "Mutate the sample table of a mesaDimRed",
      "topics": [
        "mutate.mesaDimRed"
      ]
    },
    {
      "page": "mutate.qseaSet",
      "title": "Mutate columns in a qseaSet sample table",
      "topics": [
        "mutate.qseaSet"
      ]
    },
    {
      "page": "pivotDMRsLonger",
      "title": "Transform DMR results to long format",
      "concept": [
        "DMR-helpers"
      ],
      "topics": [
        "pivotDMRsLonger"
      ]
    },
    {
      "page": "plotCNVheatmap",
      "title": "CNV heatmap across samples",
      "concept": [
        "CNV"
      ],
      "topics": [
        "plotCNVheatmap"
      ]
    },
    {
      "page": "plotCorrelationMatrix",
      "title": "Sample correlation heatmap",
      "concept": [
        "heatmaps"
      ],
      "topics": [
        "plotCorrelationMatrix"
      ]
    },
    {
      "page": "plotDimRed",
      "title": "Plot dimensionality reduction results",
      "concept": [
        "dimred-helpers"
      ],
      "topics": [
        "plotDimRed"
      ]
    },
    {
      "page": "plotDMRUpset",
      "title": "UpSet plot of DMR overlaps",
      "concept": [
        "dmr-plots"
      ],
      "topics": [
        "plotDMRUpset"
      ]
    },
    {
      "page": "plotGeneHeatmap",
      "title": "Plot sample signal over windows spanning a gene (± flanks) as a heatmap using *ComplexHeatmap*. The gene can be given as a HGNC symbol or Ensembl ID.",
      "topics": [
        "plotGeneHeatmap"
      ]
    },
    {
      "page": "plotGenomicFeatureDistribution",
      "title": "Distribution of windows across genomic features",
      "concept": [
        "annotation-summaries"
      ],
      "topics": [
        "plotGenomicFeatureDistribution"
      ]
    },
    {
      "page": "plotPCA.mesaDimRed",
      "title": "Plot principal component analysis (PCA) results",
      "concept": [
        "dimred-plotting"
      ],
      "topics": [
        "plotPCA.mesaDimRed"
      ]
    },
    {
      "page": "plotRegionsHeatmap",
      "title": "Heatmap of signal across selected genomic regions",
      "topics": [
        "plotRegionsHeatmap"
      ]
    },
    {
      "page": "plotUMAP",
      "title": "Plot UMAP results",
      "concept": [
        "dimred-helpers"
      ],
      "topics": [
        "plotUMAP"
      ]
    },
    {
      "page": "poolSamples",
      "title": "Pool (merge) samples that share a common name prefix",
      "topics": [
        "poolSamples"
      ]
    },
    {
      "page": "pull.qseaSet",
      "title": "Pull a column from a qseaSet sample table",
      "topics": [
        "pull.qseaSet"
      ]
    },
    {
      "page": "qseaTableToChrGRanges",
      "title": "Convert a makeTable-like data frame to GRanges (UCSC style)",
      "topics": [
        "qseaTableToChrGRanges"
      ]
    },
    {
      "page": "removeCNV",
      "title": "Remove (zero out) CNV data from a qseaSet",
      "concept": [
        "CNV"
      ],
      "topics": [
        "removeCNV"
      ]
    },
    {
      "page": "removeLibraryFactors",
      "title": "Set library factors to 1",
      "concept": [
        "table-helpers"
      ],
      "topics": [
        "removeLibraryFactors"
      ]
    },
    {
      "page": "removeNormMethodSuffix",
      "title": "Remove normalisation suffix from column names",
      "concept": [
        "table-helpers"
      ],
      "topics": [
        "removeNormMethodSuffix"
      ]
    },
    {
      "page": "renameQsetNames",
      "title": "Rename samples in a qseaSet by regex",
      "topics": [
        "renameQsetNames"
      ]
    },
    {
      "page": "renameSamples",
      "title": "Rename samples using a column from the sample table",
      "topics": [
        "renameSamples"
      ]
    },
    {
      "page": "runHMMCopy",
      "title": "Run HMMcopy on per-window reads for a single sample",
      "concept": [
        "CNV"
      ],
      "topics": [
        "runHMMCopy"
      ]
    },
    {
      "page": "select.qseaSet",
      "title": "Select or rename columns in a qseaSet sample table",
      "topics": [
        "select.qseaSet"
      ]
    },
    {
      "page": "selectQset",
      "title": "Select or rename columns of a qseaSet sample table",
      "topics": [
        "selectQset"
      ]
    },
    {
      "page": "setMart",
      "title": "Set or get an Ensembl/BioMart handle on a qseaSet",
      "topics": [
        "getMart",
        "getMart,qseaSet-method",
        "setMart",
        "setMart,qseaSet-method"
      ]
    },
    {
      "page": "setMesaAnnoDb",
      "title": "Set default OrgDb (annoDb) for downstream annotation helpers",
      "topics": [
        "setMesaAnnoDb"
      ]
    },
    {
      "page": "setMesaGenome",
      "title": "Set default genome for downstream annotation helpers",
      "topics": [
        "setMesaGenome"
      ]
    },
    {
      "page": "setMesaParallel",
      "title": "Manage mesa parallelisation (set & query)",
      "topics": [
        "getMesaParallel",
        "setMesaParallel"
      ]
    },
    {
      "page": "setMesaTxDb",
      "title": "Set default TxDb for downstream annotation helpers",
      "topics": [
        "setMesaTxDb"
      ]
    },
    {
      "page": "sliceDMRs",
      "title": "Take the top most DMRs per contrast, based on those with the largest value of the selected metric",
      "topics": [
        "sliceDMRs"
      ]
    },
    {
      "page": "sort.qseaSet",
      "title": "Sort samples in a qseaSet",
      "topics": [
        "sort.qseaSet"
      ]
    },
    {
      "page": "subsetQset",
      "title": "Subset a qseaSet by samples",
      "topics": [
        "subsetQset"
      ]
    },
    {
      "page": "subsetWindowsBySignal",
      "title": "Subset windows in a qseaSet by signal across samples",
      "concept": [
        "window-helpers"
      ],
      "topics": [
        "subsetWindowsBySignal"
      ]
    },
    {
      "page": "subsetWindowsOverBackground",
      "title": "Subset windows above Poisson background",
      "concept": [
        "window-helpers"
      ],
      "topics": [
        "subsetWindowsOverBackground"
      ]
    },
    {
      "page": "summariseAcrossWindows",
      "title": "Summarise across windows per sample",
      "concept": [
        "window-summaries"
      ],
      "topics": [
        "summariseAcrossWindows"
      ]
    },
    {
      "page": "summariseDMRsByContrast",
      "title": "Summarise DMRs by contrast",
      "concept": [
        "DMR-helpers"
      ],
      "topics": [
        "summariseDMRsByContrast"
      ]
    },
    {
      "page": "summariseDMRsByGene",
      "title": "Summarise DMRs by gene",
      "concept": [
        "DMR-helpers"
      ],
      "topics": [
        "summariseDMRsByGene"
      ]
    },
    {
      "page": "writeBigWigs",
      "title": "Write bigWig tracks per sample or group",
      "concept": [
        "io"
      ],
      "topics": [
        "writeBigWigs"
      ]
    },
    {
      "page": "writeDMRsToBed",
      "title": "Write DMR results to BED files",
      "concept": [
        "DMR-helpers"
      ],
      "topics": [
        "writeDMRsToBed"
      ]
    },
    {
      "page": "writeDMRsToExcel",
      "title": "Write DMR results to an Excel workbook",
      "concept": [
        "DMR-helpers"
      ],
      "topics": [
        "writeDMRsToExcel"
      ]
    }
  ],
  "_readme": "https://github.com/BiocStaging/mesa/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "ape",
    "aplot",
    "askpass",
    "base64enc",
    "BH",
    "Biobase",
    "BiocBaseUtils",
    "BiocFileCache",
    "BiocGenerics",
    "BiocIO",
    "BiocParallel",
    "biomaRt",
    "Biostrings",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "boot",
    "BSgenome",
    "bslib",
    "cachem",
    "caTools",
    "ChIPseeker",
    "cigarillo",
    "circlize",
    "cli",
    "clipr",
    "clue",
    "cluster",
    "codetools",
    "colorspace",
    "ComplexHeatmap",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "digest",
    "doParallel",
    "DOSE",
    "dplyr",
    "enrichit",
    "enrichplot",
    "evaluate",
    "farver",
    "fastmap",
    "filelock",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "foreach",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "gdtools",
    "generics",
    "GenomeInfoDb",
    "GenomicAlignments",
    "GenomicFeatures",
    "GenomicRanges",
    "GetoptLong",
    "ggforce",
    "ggfun",
    "ggiraph",
    "ggnewscale",
    "ggplot2",
    "ggplotify",
    "ggrepel",
    "ggtangle",
    "ggtree",
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