{ "_id": "6a1ad4f11d7bb097a09e45b4", "Package": "DMCHMM", "Type": "Package", "Title": "Differentially Methylated CpG using Hidden Markov Model", "Version": "1.35.0", "Authors@R": "c(person(\"Farhad\", \"Shokoohi\", role = c(\"aut\", \"cre\"),\nemail = \"shokoohi@icloud.com\", comment = c(ORCID = \"0000-0002-6224-2609\"))\n)", "Author": "Farhad Shokoohi", "Maintainer": "Farhad Shokoohi ", "Description": "A pipeline for identifying differentially methylated CpG\nsites using Hidden Markov Model in bisulfite sequencing data.\nDNA methylation studies have enabled researchers to understand\nmethylation patterns and their regulatory roles in biological\nprocesses and disease. However, only a limited number of\nstatistical approaches have been developed to provide formal\nquantitative analysis. Specifically, a few available methods do\nidentify differentially methylated CpG (DMC) sites or regions\n(DMR), but they suffer from limitations that arise mostly due\nto challenges inherent in bisulfite sequencing data. These\nchallenges include: (1) that read-depths vary considerably\namong genomic positions and are often low; (2) both methylation\nand autocorrelation patterns change as regions change; and (3)\nCpG sites are distributed unevenly. Furthermore, there are\nseveral methodological limitations: almost none of these tools\nis capable of comparing multiple groups and/or working with\nmissing values, and only a few allow continuous or multiple\ncovariates. The last of these is of great interest among\nresearchers, as the goal is often to find which regions of the\ngenome are associated with several exposures and traits. To\ntackle these issues, we have developed an efficient DMC\nidentification method based on Hidden Markov Models (HMMs)\ncalled “DMCHMM” which is a three-step approach (model\nselection, prediction, testing) aiming to address the\naforementioned drawbacks.", "VignetteBuilder": "knitr", "biocViews": "DifferentialMethylation, Sequencing, HiddenMarkovModel,\nCoverage", "License": "GPL-3", "Date": "2020-09-27", "Encoding": "UTF-8", "BugReports": "https://github.com/shokoohi/DMCHMM/issues", "RoxygenNote": "7.1.2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:41:04 UTC", "User": "root" }, "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:46:17 UTC", "RemoteUrl": "https://github.com/bioc/DMCHMM", "RemoteRef": "HEAD", "RemoteSha": "8b29483b6466da51de8cfef585c800adb625fc69", "MD5sum": "06336282a277378b12f84fd7622e017f", "_user": "bioc", "_type": "src", 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