{ "_id": "6a1ac2a11d7bb097a09d9e2c", "Package": "MethTargetedNGS", "Type": "Package", "Title": "Perform Methylation Analysis on Next Generation Sequencing Data", "Version": "1.45.0", "Date": "2024-04-23", "SystemRequirements": "HMMER3", "Author": "Muhammad Ahmer Jamil with Contribution of Prof. Holger Frohlich\nand Priv.-Doz. Dr. Osman El-Maarri", "Maintainer": "Muhammad Ahmer Jamil ", "Description": "Perform step by step methylation analysis of Next\nGeneration Sequencing data.", "License": "Artistic-2.0", "biocViews": "ResearchField, Genetics, Sequencing, Alignment,\nSequenceMatching, DataImport", "Config/pak/sysreqs": "libicu-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:41:08 UTC", "RemoteUrl": "https://github.com/bioc/MethTargetedNGS", "RemoteRef": "HEAD", "RemoteSha": "8733b6e58a9d38176d387e33ce5ee30fb6364172", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:38:12 UTC", "User": "root" }, "MD5sum": "6a880456cb5fdeecaafeb700d90d929e", "_user": "bioc", "_type": "src", "_file": "MethTargetedNGS_1.45.0.tar.gz", "_fileid": "585f81227eca5835c0f4b514c14c055af6be53f88cc400059d115c77a858ea01", "_filesize": 248604, "_sha256": "585f81227eca5835c0f4b514c14c055af6be53f88cc400059d115c77a858ea01", "_created": "2026-05-30T07:38:12.000Z", "_published": "2026-05-30T10:57:37.627Z", "_jobs": [ { "job": 78634062945, "time": 171, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306551934" }, { "job": 78634062959, "time": 233, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306558241" }, { "job": 78634062967, "time": 225, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306557475" }, { "job": 78634062969, "time": 151, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307660245" }, { "job": 78634062963, "time": 140, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307659125" }, { "job": 78633877402, "time": 218, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306534374" }, { "job": 78634062944, "time": 116, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306546297" }, { "job": 78634062964, "time": 154, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306550242" }, { "job": 78634062971, "time": 158, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306550834" }, { "job": 78634062972, "time": 152, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306549986" } ], "_bioccheck": { "error": 2, "warning": 1, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678203049", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/MethTargetedNGS", "_commit": { "id": "8733b6e58a9d38176d387e33ce5ee30fb6364172", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380068 }, "_maintainer": { "name": "Muhammad Ahmer Jamil", "email": "engr.ahmerjamil@gmail.com", "login": "ahmerjamil88", "description": "", "uuid": 10399618 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.2", "role": "Depends" }, { "package": "stringr", "role": "Depends" }, { "package": "seqinr", "role": "Depends" }, { "package": "gplots", "role": "Depends" }, { "package": "Biostrings", "role": "Depends" }, { "package": "pwalign", "role": "Depends" }, { "package": "utils", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.45.0", "bioc": "3.24" }, { "branch": "release", "version": "1.44.0", "bioc": "3.23" } ], "_topics": [ "researchfield", "genetics", "sequencing", "alignment", "sequencematching", "dataimport" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 340, "source": "https://www.bioconductor.org/packages/stats/bioc/MethTargetedNGS" }, "_mentions": 1, "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MethTargetedNGS.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "bconv", "compare_samples", "fishertest_cpg", "hmmbuild", "methAlign", "methAvg", "methEntropy", "methHeatmap", "nhmmer", "odd_ratio" ], "_help": [ { "page": "MethTargetedNGS-package", "title": "Methylation Analysis of Next Generation Sequencing data.", "topics": [ "MethTargetedNGS-package", "MethTargetedNGS" ] }, { "page": "bconv", "title": "Convert non-bisulfite sequences to bisulfite sequences.", "topics": [ "bconv" ] }, { "page": "compare_samples", "title": "Complete Methylation Analysis of Next Generation Sequencing Data", "topics": [ "compare_samples" ] }, { "page": "fishertest_cpg", "title": "Perform Fisher Exact Test on Methylation Data.", "topics": [ "fishertest_cpg" ] }, { "page": "hmmbuild", "title": "Create Profile Hidden Markov Model of given aligned sequences", "topics": [ "hmmbuild" ] }, { "page": "methAlign", "title": "Align sequences with the reference sequence using pairwiseAlignment function from the pwalign package", "topics": [ "methAlign" ] }, { "page": "methAvg", "title": "Calculate Methylation Average of given methylation matrix", "topics": [ "methAvg" ] }, { "page": "methEntropy", "title": "Calculate Methylation Entropy", "topics": [ "methEntropy" ] }, { "page": "methHeatmap", "title": "Generate Heatmap of the given methylation data.", "topics": [ "methHeatmap" ] }, { "page": "nhmmer", "title": "Calculate likelihood of the given profile hidden markov model against group of sequences", "topics": [ "nhmmer" ] }, { "page": "odd_ratio", "title": "Calculate log odd ratio of the given samples (healthy/tumor)", "topics": [ "odd_ratio" ] } ], "_rundeps": [ "ade4", "BiocGenerics", "Biostrings", "bitops", "caTools", "cli", "crayon", "generics", "glue", "gplots", "gtools", "IRanges", "KernSmooth", "lattice", "lifecycle", "magrittr", "MASS", "nlme", "pixmap", "pwalign", "Rcpp", "RcppArmadillo", "rlang", "S4Vectors", "segmented", "Seqinfo", "seqinr", "sp", "stringi", "stringr", "vctrs", "XVector" ], "_vignettes": [ { "source": "MethTargetedNGS.Rnw", "filename": "MethTargetedNGS.pdf", "title": "Introduction to MethTargetedNGS", "engine": "utils::Sweave", "headings": [], "created": "2015-04-03 20:49:01", "modified": "2015-04-03 20:49:01", "commits": 1 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "methtargetedngs", "_universes": [ "bioc", "ahmerjamil88" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.45.0", "date": "2026-05-30T07:41:26.000Z", "distro": "noble", "commit": "8733b6e58a9d38176d387e33ce5ee30fb6364172", "fileid": "c8954a6f35acd8741f5ffb5bd9a9aaeaeaa7ecd88a1055b72065ba31c4f2fcc0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678203049" }, { "r": "4.6.0", "os": "linux", "version": "1.45.0", "date": "2026-05-30T07:41:19.000Z", "distro": "noble", "commit": "8733b6e58a9d38176d387e33ce5ee30fb6364172", "fileid": "0a7a732dd0b44de9da55bc0093d6b4a3a5c45e8f53810fad07e388bf5ee2e6e9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678203049" }, { "r": "4.5.3", "os": "mac", "version": "1.45.0", "date": "2026-05-30T10:53:05.000Z", "commit": "8733b6e58a9d38176d387e33ce5ee30fb6364172", "fileid": "e961fba71f20f82db14c9cc5cc099afe4035723c9c2b50a607905f5c7585ef28", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678203049" }, { "r": "4.6.0", "os": "mac", "version": "1.45.0", "date": "2026-05-30T10:52:52.000Z", "commit": "8733b6e58a9d38176d387e33ce5ee30fb6364172", "fileid": "66e0f26010c88a7008f27792c4c2c48c273cb7c9cde0440514f4c10017caccd6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678203049" }, { "r": "4.6.0", "os": "wasm", "version": "1.45.0", "date": "2026-05-30T07:40:30.000Z", "commit": "8733b6e58a9d38176d387e33ce5ee30fb6364172", "fileid": "2b11a053e47c2eacc80febef870857306d868211ad5ce13150d5b52bc7babb4c", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678203049" }, { "r": "4.7.0", "os": "win", "version": "1.45.0", "date": "2026-05-30T07:40:14.000Z", "commit": "8733b6e58a9d38176d387e33ce5ee30fb6364172", "fileid": "4d0cb943887808f465b4b9f891925afb85df8ef20b378dc82a5611fbdb1ab322", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678203049" }, { "r": "4.5.3", "os": "win", "version": "1.45.0", "date": "2026-05-30T07:40:05.000Z", "commit": "8733b6e58a9d38176d387e33ce5ee30fb6364172", "fileid": "19156f48e42efe378e3beaafaddf40d8c9224d270c7e20bc8d4697f646cace55", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678203049" }, { "r": "4.6.0", "os": "win", "version": "1.45.0", "date": "2026-05-30T07:40:00.000Z", "commit": "8733b6e58a9d38176d387e33ce5ee30fb6364172", "fileid": "c0e53e463f5c76da8ec5fe7b493f03fc166a56f535064b6221c314fadff46343", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678203049" } ] }