{ "_id": "6a49a3a1162b78b26a584735", "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", "RoxygenNote": "7.2.3", "biocViews": "DNAMethylation, DifferentialMethylation, ImmunoOncology,\nBiomedicalInformatics, MethylationArray, Software,\nMultipleComparison, Sequencing, Spatial, Coverage, GeneTarget,\nHiddenMarkovModel, Microarray", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:02:06 UTC", "RemoteUrl": "https://github.com/bioc/betaHMM", "RemoteRef": "HEAD", "RemoteSha": "a81397575e827616c5117ba45b560b22d2d2ae35", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-05 00:10:54 UTC", "User": "root" }, "Author": "Koyel Majumdar [cre, aut] (ORCID:\n),\nRomina Silva [aut],\nAntoinette Sabrina Perry [aut],\nRonald William Watson [aut],\nIsobel Claire Gorley [aut] (ORCID:\n),\nThomas Brendan Murphy [aut] (ORCID:\n),\nFlorence Jaffrezic [aut],\nAndrea Rau [aut] (ORCID: )", "Maintainer": "Koyel Majumdar ", "_user": "bioc", "_type": "src", "_file": "betaHMM_1.9.0.tar.gz", "_fileid": "https://r2.ropensci.org/ff143f4aaedd32a01e44ce21351e379c3dda1d0e7535a9b308bfe45e097b1136", "_filesize": 3924125, "_sha256": "ff143f4aaedd32a01e44ce21351e379c3dda1d0e7535a9b308bfe45e097b1136", "_expires": "2026-10-13T00:21:51.000Z", "_created": "2026-07-05T00:10:54.000Z", "_published": "2026-07-05T00:21:53.699Z", "_bioccheck": { "error": 0, "warning": 0, "note": 5 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28723861725", "_status": "success", "_upstream": "https://github.com/bioc/betaHMM", "_commit": { "id": "a81397575e827616c5117ba45b560b22d2d2ae35", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381326 }, "_maintainer": { "name": "Koyel Majumdar", "email": "koyelmajumdar.phdresearch@gmail.com", "login": "koyelucd", "linkedin": "in/koyel-majumdar-0b261b154", "description": "Ph.D. Researcher in SFI CRT at University College Dublin. My current research revolves around developing statistical models for analysing DNA methylation data.", "uuid": 94002124, "orcid": "0000-0001-6469-488X" }, "_distro": "resolute", "_jobs": [ { "job": 85178061207, "time": 179, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8086643456" }, { "job": 85178061215, "time": 598, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8086683083" }, { "job": 85178061222, "time": 565, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8086679715" }, { "job": 85178061217, "time": 320, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8086656232" }, { "job": 85178061218, "time": 299, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8086654391" }, { "job": 85177670020, "time": 417, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8086626130" }, { "job": 85178061211, "time": 162, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8086641861" }, { "job": 85178061214, "time": 522, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8086674890" }, { "job": 85178061253, "time": 518, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8086674816" }, { "job": 85178061254, "time": 492, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8086671092" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3.0", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "S4Vectors", "role": "Depends" }, { "package": "GenomicRanges", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "pROC", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-38", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.9.0", "bioc": "3.24" }, { "branch": "release", "version": "1.8.0", "bioc": "3.23" } ], "_topics": [ "dnamethylation", "differentialmethylation", "immunooncology", "biomedicalinformatics", "methylationarray", "software", "multiplecomparison", "sequencing", "spatial", "coverage", "genetarget", "hiddenmarkovmodel", "microarray" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 9, "_rbuild": "4.6.1", "_assets": [ "extra/betaHMM.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/koyelucd/betahmm", "_realowner": "bioc", "_cranurl": false, "_exports": [ "A", "annotatedData", "AUC", "betaHMM", "betaHMMResults", "betaHMMrun", "chromosome_number", "dmc_identification", "dmc_identification_run", "dmcResults", "dmr_identification", "dmr_identification_run", "dmrResults", "hidden_states", "K", "llk", "model_parameters", "N", "phi", "plot", "R", "summary", "tau", "threshold", "threshold_identification", "threshold_identification_run", "threshold_Results", "treatment_group", "uncertainty" ], "_datasets": [ { "name": "annotation_data", "title": "MethylationEPIC manifest data.", "object": "annotation_data", "file": "annotation_data.rda", "class": [ "data.frame" ], "fields": [ "IlmnID", "Genome_Build", "CHR", "MAPINFO", "UCSC_RefGene_Name", "UCSC_RefGene_Accession", "UCSC_RefGene_Group", "UCSC_CpG_Islands_Name", "Relation_to_UCSC_CpG_Island" ], "rows": 38672, "table": true, "tojson": true }, { "name": "pca_methylation_data", "title": "Simulated DNA methylation data", "object": "pca_methylation_data", "file": "pca_methylation_data.rda", "class": [ "data.frame" ], "fields": [ "IlmnID", "FFPE_benign_1", "FFPE_benign_2", "FFPE_benign_3", "FFPE_benign_4", "FFPE_tumour_1", "FFPE_tumour_2", "FFPE_tumour_3", "FFPE_tumour_4" ], "rows": 38672, "table": true, "tojson": true }, { "name": "sample_annotation_file", "title": "MethylationEPIC manifest data.", "object": "sample_annotation_file", "file": "sample_annotation_file.rda", "class": [ "data.frame" ], "fields": [ "IlmnID", "Genome_Build", "CHR", "MAPINFO", "UCSC_RefGene_Name", "UCSC_RefGene_Accession", "UCSC_RefGene_Group", "UCSC_CpG_Islands_Name", "Relation_to_UCSC_CpG_Island" ], "rows": 100, "table": true, "tojson": true }, { "name": "sample_methylation_file", "title": "Simulated DNA methylation data", "object": "sample_methylation_file", "file": "sample_methylation_file.rda", "class": [ "data.frame" ], "fields": [ "IlmnID", "Benign_Patient_1", "Benign_Patient_2", "Benign_Patient_3", "Benign_Patient_4", "Tumour_Patient_1", "Tumour_Patient_2", "Tumour_Patient_3", "Tumour_Patient_4" ], "rows": 100, "table": true, "tojson": true } ], "_help": [ { "page": "packageHelpers", "title": "Accessors for the betaHMM package.", "topics": [ "A", "A,betaHMMResults-method", "A,NULL-method", "A,RangedSummarizedExperiment-method", "annotatedData", "annotatedData,betaHMMResults-method", "annotatedData,threshold_Results-method", "AUC", "AUC,dmcResults-method", "AUC,NULL-method", "AUC,RangedSummarizedExperiment-method", "chromosome_number", "chromosome_number,betaHMMResults-method", "chromosome_number,dmrResults-method", "chromosome_number,NULL-method", "chromosome_number,RangedSummarizedExperiment-method", "hidden_states", "hidden_states,betaHMMResults-method", "hidden_states,NULL-method", "hidden_states,RangedSummarizedExperiment-method", "hidden_states,threshold_Results-method", "K", "K,betaHMMResults-method", "K,dmcResults-method", "K,NULL-method", "K,RangedSummarizedExperiment-method", "K,threshold_Results-method", "llk", "llk,betaHMMResults-method", "llk,NULL-method", "llk,RangedSummarizedExperiment-method", "model_parameters", "model_parameters,NULL-method", "model_parameters,RangedSummarizedExperiment-method", "model_parameters,threshold_Results-method", "N", "N,betaHMMResults-method", "N,dmcResults-method", "N,NULL-method", "N,RangedSummarizedExperiment-method", "phi", "phi,betaHMMResults-method", "phi,NULL-method", "phi,RangedSummarizedExperiment-method", "phi,threshold_Results-method", "R", "R,betaHMMResults-method", "R,dmcResults-method", "R,NULL-method", "R,RangedSummarizedExperiment-method", "tau", "tau,betaHMMResults-method", "tau,NULL-method", "tau,RangedSummarizedExperiment-method", "threshold", "threshold,NULL-method", "threshold,RangedSummarizedExperiment-method", "threshold,threshold_Results-method", "treatment_group", "treatment_group,betaHMMResults-method", "treatment_group,dmcResults-method", "treatment_group,NULL-method", "treatment_group,RangedSummarizedExperiment-method", "uncertainty", "uncertainty,dmcResults-method", "uncertainty,NULL-method", "uncertainty,RangedSummarizedExperiment-method" ] }, { "page": "annotation_data", "title": "MethylationEPIC manifest data.", "topics": [ "annotation_data" ] }, { "page": "betaHMM", "title": "HMM for beta valued DNA data", "topics": [ "betaHMM", "betaHMM,data.frame,data.frame-method", "betaHMM,data.frame,GRanges-method", "betaHMM,data.frame,matrix-method", "betaHMM,data.frame,RangedSummarizedExperiment-method", "betaHMM,data.frame,RangedSummarizedExperiment.-method", "betaHMM,GRanges,data.frame-method", "betaHMM,GRanges,GRanges-method", "betaHMM,GRanges,matrix-method", "betaHMM,GRanges,RangedSummarizedExperiment-method", "betaHMM,matrix,data.frame-method", "betaHMM,matrix,GRanges-method", "betaHMM,matrix,matrix-method", "betaHMM,matrix,RangedSummarizedExperiment-method", "betaHMM,matrix,RangedSummarizedExperiment.-method", "betaHMM,RangedSummarizedExperiment,data.frame-method", "betaHMM,RangedSummarizedExperiment,GRanges-method", "betaHMM,RangedSummarizedExperiment,matrix-method", "betaHMM,RangedSummarizedExperiment,RangedSummarizedExperiment-method", "betaHMM,RangedSummarizedExperiment,RangedSummarizedExperiment.-method", "betaHMM-methods" ] }, { "page": "betaHMMResults", "title": "betaHMMResults object and constructor", "topics": [ "betaHMMResults", "betaHMMResults-class" ] }, { "page": "betaHMMrun", "title": "The betaHMM model parameter estimation function", "topics": [ "betaHMMrun" ] }, { "page": "dmc_identification", "title": "DMC identification from estimated betaHMM model parameters", "topics": [ "dmc_identification", "dmc_identification,betaHMMResults-method", "dmc_identification-methods" ] }, { "page": "dmc_identification_run", "title": "DMC identification from estimated betaHMM model parameters", "topics": [ "dmc_identification_run" ] }, { "page": "dmcResults", "title": "dmcResults object and constructor", "topics": [ "dmcResults", "dmcResults-class" ] }, { "page": "dmr_identification", "title": "DMR identification from DMCs identified", "topics": [ "dmr_identification", "dmr_identification,data.frame-method", "dmr_identification,dmcResults-method", "dmr_identification,matrix-method", "dmr_identification-methods" ] }, { "page": "dmr_identification_run", "title": "DMR identification from DMCs identified", "topics": [ "dmr_identification_run" ] }, { "page": "dmrResults", "title": "dmrResults object and constructor", "topics": [ "dmrResults", "dmrResults-class" ] }, { "page": "pca_methylation_data", "title": "Simulated DNA methylation data", "topics": [ "pca_methylation_data" ] }, { "page": "plot", "title": "Visualize results from 'betaHMM'/ 'dmc_identification'/ 'threshold_identification' functions.", "topics": [ "plot", "plot,betaHMMResults-method", "plot,dmcResults-method", "plot,threshold_Results-method", "plot-methods" ] }, { "page": "sample_annotation_file", "title": "MethylationEPIC manifest data.", "topics": [ "sample_annotation_file" ] }, { "page": "sample_methylation_file", "title": "Simulated DNA methylation data", "topics": [ "sample_methylation_file" ] }, { "page": "summary", "title": "Summarize results from the three betaHMM workflow functions", "topics": [ "summary", "summary,betaHMMResults-method", "summary,dmcResults-method", "summary,dmrResults-method", "summary-methods" ] }, { "page": "threshold_identification", "title": "HMM for beta valued DNA data for a single treatment condition", "topics": [ "threshold_identification", "threshold_identification,data.frame-method", "threshold_identification,matrix-method", "threshold_identification-methods" ] }, { "page": "threshold_identification_run", "title": "Threshold indentification function", "topics": [ "threshold_identification_run" ] }, { "page": "threshold_Results", "title": "threshold_Results object and constructor", "topics": [ "threshold_Results", "threshold_Results-class" ] } ], "_readme": "https://github.com/bioc/betaHMM/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "cli", "codetools", "cowplot", "cpp11", "DelayedArray", "doParallel", "dplyr", "farver", "foreach", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "IRanges", "isoband", "iterators", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "pillar", "pkgconfig", "pROC", "purrr", "R6", "RColorBrewer", "Rcpp", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "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", "modified": "2023-11-22 07:30:16", "commits": 2 } ], "_score": 4.176091259055681, "_indexed": true, "_nocasepkg": "betahmm", "_universes": [ "bioc", "koyelucd" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.9.0", "date": "2026-07-05T00:14:04.000Z", "distro": "resolute", "commit": "a81397575e827616c5117ba45b560b22d2d2ae35", "fileid": "https://r2.ropensci.org/e14bcdcadb8c78c34471844d1534bd4a266dbbe432db62610b7c67868e357212", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723861725" }, { "r": "4.6.1", "os": "linux", "version": "1.9.0", "date": "2026-07-05T00:14:12.000Z", "distro": "resolute", "commit": "a81397575e827616c5117ba45b560b22d2d2ae35", "fileid": "https://r2.ropensci.org/aec369600ab5e50f63a189390b6ce514a9d2fb6da67c3fab874077e84b566405", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723861725" }, { "r": "4.5.3", "os": "mac", "version": "1.9.0", "date": "2026-07-05T00:12:39.000Z", "commit": "a81397575e827616c5117ba45b560b22d2d2ae35", "fileid": "https://r2.ropensci.org/0d6d67a524c0edb6a10ce0225c7eabe0801dd8a72952244cf0f78b58622545bc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723861725" }, { "r": "4.6.1", "os": "mac", "version": "1.9.0", "date": "2026-07-05T00:12:41.000Z", "commit": "a81397575e827616c5117ba45b560b22d2d2ae35", "fileid": "https://r2.ropensci.org/34a1a0195efa6a7f2d466e271de345b79bf34b0e7fe610967c418d9c0abed2ff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723861725" }, { "r": "4.6.0", "os": "wasm", "version": "1.9.0", "date": "2026-07-05T00:14:13.000Z", "commit": "a81397575e827616c5117ba45b560b22d2d2ae35", "fileid": "https://r2.ropensci.org/f022ff166141c5cab97d6cf4cc94fc27d371d2d6da02a3aa00ecb040e2d56e42", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723861725" }, { "r": "4.7.0", "os": "win", "version": "1.9.0", "date": "2026-07-05T00:12:32.000Z", "commit": "a81397575e827616c5117ba45b560b22d2d2ae35", "fileid": "https://r2.ropensci.org/3e83d6dbd4bfa5b91b9bfb6f7460f90d312ec1010540d92ea64e8d3a190f055a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723861725" }, { "r": "4.5.3", "os": "win", "version": "1.9.0", "date": "2026-07-05T00:12:42.000Z", "commit": "a81397575e827616c5117ba45b560b22d2d2ae35", "fileid": "https://r2.ropensci.org/229e1c5bf28d4f80211957f93d476e9eed7d2bef4ac244db43dcdff4699e7d53", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723861725" }, { "r": "4.6.1", "os": "win", "version": "1.9.0", "date": "2026-07-05T00:12:36.000Z", "commit": "a81397575e827616c5117ba45b560b22d2d2ae35", "fileid": "https://r2.ropensci.org/4c10506a3c522acf880c1df7a2de5fb61e6ee7e81659c268b61310c4c3f72922", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28723861725" } ] }