{
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  "Package": "betaHMM",
  "Type": "Package",
  "Title": "A Hidden Markov Model Approach for Identifying Differentially\nMethylated Sites and Regions for Beta-Valued DNA Methylation\nData",
  "Version": "1.9.0",
  "Authors@R": "c(person(\"Koyel\",\"Majumdar\",email=\"koyelmajumdar.phdresearch@gmail.com\",\nrole=c(\"cre\",\"aut\"),comment = c(ORCID = \"0000-0001-6469-488X\")),\nperson(\"Romina\",\"Silva\",\nrole=\"aut\"),\nperson(\"Antoinette Sabrina\",\"Perry\",\nrole=\"aut\"),\nperson(\"Ronald William\",\"Watson\",\nrole=\"aut\"),\nperson(\"Isobel Claire\",\"Gorley\",email=\"claire.gormley@ucd.ie\",\nrole=\"aut\", comment=c(ORCID=\"0000-0001-7713-681X\")),\nperson(\"Thomas Brendan\",\"Murphy\",email=\"brendan.murphy@ucd.ie\",\nrole=\"aut\",comment=c(ORCID=\"0000-0002-5668-7046\")),\nperson(\"Florence\",\"Jaffrezic\",email=\"florence.jaffrezic@inrae.fr\",\nrole=\"aut\"),\nperson(\"Andrea\",\"Rau\",email=\"andrea.rau@inrae.fr\",role=\"aut\",\ncomment = c(ORCID = \"0000-0001-6469-488X\")))",
  "Description": "A novel approach utilizing a homogeneous hidden Markov\nmodel. And effectively model untransformed beta values. To\nidentify DMCs while considering the spatial. Correlation of the\nadjacent CpG sites.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
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  "biocViews": "DNAMethylation, DifferentialMethylation, ImmunoOncology,\nBiomedicalInformatics, MethylationArray, Software,\nMultipleComparison, Sequencing, Spatial, Coverage, GeneTarget,\nHiddenMarkovModel, Microarray",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:02:06 UTC",
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  "Author": "Koyel Majumdar [cre, aut] (ORCID:\n<https://orcid.org/0000-0001-6469-488X>),\nRomina Silva [aut],\nAntoinette Sabrina Perry [aut],\nRonald William Watson [aut],\nIsobel Claire Gorley [aut] (ORCID:\n<https://orcid.org/0000-0001-7713-681X>),\nThomas Brendan Murphy [aut] (ORCID:\n<https://orcid.org/0000-0002-5668-7046>),\nFlorence Jaffrezic [aut],\nAndrea Rau [aut] (ORCID: <https://orcid.org/0000-0001-6469-488X>)",
  "Maintainer": "Koyel Majumdar <koyelmajumdar.phdresearch@gmail.com>",
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  "_created": "2026-10-03T07:04:35.000Z",
  "_published": "2026-10-03T07:16:24.083Z",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
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    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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  "_vignettes": [
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      "source": "betaHMM.Rmd",
      "filename": "betaHMM.html",
      "title": "betaHMM package: Quick-start guide",
      "author": "Koyel Majumdar, Isobel Claire Gormley, Thomas Brendan Murphy, Romina Silva, Antoinette Sabrina Perry, Ronald William Watson, Florence Jaffrézic, Andrea Rau",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Introduction",
        "Walk through",
        "Prerequisites",
        "Loading the data",
        "Loading the methylation and annotation data",
        "The betaHMM workflow",
        "Model parameter estimation",
        "Summary of model parameters",
        "DMC identification",
        "Summary of the DMCs identified",
        "Plot the density estimates of the model parameter estimates",
        "DMR identification from DMCs identified",
        "Summary of the DMRs identified",
        "Plot to visualise the DMCs and DMRs",
        "Threshold identification in DNA samples belonging to a specific condition",
        "Plotting the results from threshold identification function"
      ],
      "created": "2023-10-09 09:04:59",
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