{ "_id": "6a1acae51d7bb097a09dd9fc", "Package": "hummingbird", "Type": "Package", "Title": "Bayesian Hidden Markov Model for the detection of differentially\nmethylated regions", "Version": "1.23.0", "Authors@R": "c(person(\"Eleni\", \"Adam\", email = \"eadam002@odu.edu\", role = c(\"aut\", \"cre\")), person(\"Tieming\", \"Ji\", role = c(\"aut\")), person(\"Desh\", \"Ranjan\", role = c(\"aut\")))", "Description": "A package for detecting differential methylation. It\nexploits a Bayesian hidden Markov model that incorporates\nlocation dependence among genomic loci, unlike most existing\nmethods that assume independence among observations. Bayesian\npriors are applied to permit information sharing across an\nentire chromosome for improved power of detection. The direct\noutput of our software package is the best sequence of\nmethylation states, eliminating the use of a subjective, and\nmost of the time an arbitrary, threshold of p-value for\ndetermining significance. At last, our methodology does not\nrequire replication in either or both of the two comparison\ngroups.", "License": "GPL (>=2)", "Encoding": "UTF-8", "LazyData": "true", "biocViews": "HiddenMarkovModel, Bayesian, DNAMethylation,\nBiomedicalInformatics, Sequencing, GeneExpression,\nDifferentialExpression, DifferentialMethylation", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:53:20 UTC", "RemoteUrl": "https://github.com/bioc/hummingbird", "RemoteRef": "HEAD", "RemoteSha": "80fd0db252348953091ea66ce0947c75a8c61656", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 07:58:38 UTC", "User": "root" }, "Author": "Eleni Adam [aut, cre],\nTieming Ji [aut],\nDesh Ranjan [aut]", "Maintainer": "Eleni Adam ", "MD5sum": "d1eb218588e6e63eb9d1b1f31efe98d0", "_user": "bioc", "_type": "src", "_file": "hummingbird_1.23.0.tar.gz", "_fileid": "d19af9f98c750bded0cf33b625cb1537142201f671d9cff130608fa2f416a716", "_filesize": 381580, "_sha256": "d19af9f98c750bded0cf33b625cb1537142201f671d9cff130608fa2f416a716", "_created": "2026-05-30T07:58:38.000Z", "_published": "2026-05-30T11:32:53.845Z", "_jobs": [ { "job": 78635085289, "time": 167, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306674297" }, { "job": 78635085318, "time": 198, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7306677328" }, { "job": 78635085316, "time": 289, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306685907" }, { "job": 78635085317, "time": 233, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7306680588" }, { "job": 78635085319, "time": 276, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306684687" }, { "job": 78635085314, "time": 150, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307869130" }, { "job": 78635085305, "time": 513, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7306708770" }, { "job": 78635085297, "time": 142, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307868367" }, { "job": 78635085301, "time": 347, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306692156" }, { "job": 78634876978, "time": 241, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306657096" }, { "job": 78635085302, "time": 104, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306667762" }, { "job": 78635085296, "time": 192, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306676643" }, { "job": 78635085306, "time": 176, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306675177" }, { "job": 78635085303, "time": 220, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306679394" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678589748", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/hummingbird", "_commit": { "id": "80fd0db252348953091ea66ce0947c75a8c61656", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380800 }, "_maintainer": { "name": "Eleni Adam", "email": "eadam002@odu.edu", "login": "eleniadam", "description": "PhD Candidate in Computer Science", "uuid": 31490261 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.23.0", "bioc": "3.24" }, { "branch": "release", "version": "1.22.0", "bioc": "3.23" } ], "_topics": [ "hiddenmarkovmodel", "bayesian", "dnamethylation", "biomedicalinformatics", "sequencing", "geneexpression", "differentialexpression", "differentialmethylation", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 302, "source": "https://www.bioconductor.org/packages/stats/bioc/hummingbird" }, "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/hummingbird.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "hummingbirdEM", "hummingbirdEMinternal", "hummingbirdGraph", "hummingbirdPostAdjustment", "hummingbirdPostAdjustmentInternal" ], "_datasets": [ { "name": "abnormM", "title": "Sample matrix", "object": "exampleHummingbird", "class": [ "matrix", "array" ], "fields": {}, "rows": 4746, "table": true, "tojson": true }, { "name": "abnormUM", "title": "Sample matrix", "object": "exampleHummingbird", "class": [ "matrix", "array" ], "fields": {}, "rows": 4746, "table": true, "tojson": true }, { "name": "exampleSECase", "title": "Sample input data", "object": "exampleHummingbird", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "exampleSEControl", "title": "Sample input data", "object": "exampleHummingbird", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "normM", "title": "Sample matrix", "object": "exampleHummingbird", "class": [ "matrix", "array" ], "fields": {}, "rows": 4746, "table": true, "tojson": true }, { "name": "normUM", "title": "Sample matrix", "object": "exampleHummingbird", "class": [ "matrix", "array" ], "fields": {}, "rows": 4746, "table": true, "tojson": true }, { "name": "pos", "title": "Sample matrix", "object": "exampleHummingbird", "class": [ "matrix", "array" ], "fields": {}, "rows": 4746, "table": true, "tojson": true } ], "_help": [ { "page": "hummingbird-package", "title": "A Bayesian Hidden Markov Model for the detection of differentially methylated regions", "topics": [ "hummingbird-package", "hummingbird" ] }, { "page": "abnormM", "title": "Sample matrix", "topics": [ "abnormM" ] }, { "page": "abnormUM", "title": "Sample matrix", "topics": [ "abnormUM" ] }, { "page": "exampleHummingbird", "title": "Sample dataset", "topics": [ "exampleHummingbird" ] }, { "page": "exampleSECase", "title": "Sample input data", "topics": [ "exampleSECase" ] }, { "page": "exampleSEControl", "title": "Sample input data", "topics": [ "exampleSEControl" ] }, { "page": "hummingbirdEM", "title": "EM Algorithm for Fitting the Hidden Markov Model", "topics": [ "hummingbirdEM" ] }, { "page": "hummingbirdEMinternal", "title": "EM Algorithm (internal)", "topics": [ "hummingbirdEMinternal" ] }, { "page": "hummingbirdGraph", "title": "Observations and Predictions Graphs", "topics": [ "hummingbirdGraph" ] }, { "page": "hummingbirdPostAdjustment", "title": "Post Adjustment algorithm for the output of the EM", "topics": [ "hummingbirdPostAdjustment" ] }, { "page": "hummingbirdPostAdjustmentInternal", "title": "Post Adjustment algorithm (internal)", "topics": [ "hummingbirdPostAdjustmentInternal" ] }, { "page": "normM", "title": "Sample matrix", "topics": [ "normM" ] }, { "page": "normUM", "title": "Sample matrix", "topics": [ "normUM" ] }, { "page": "pos", "title": "Sample matrix", "topics": [ "pos" ] } ], "_readme": "https://github.com/bioc/hummingbird/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "DelayedArray", "generics", "GenomicRanges", "IRanges", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "Rcpp", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "SummarizedExperiment", "XVector" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "hummingbird.Rmd", "filename": "hummingbird.html", "title": "The hummingbird", "author": "Eleni Adam, Tieming Ji, Desh Ranjan", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Functions", "Sample Dataset", "Example", "Citation", "Reference", "Session Info" ], "created": "2020-05-15 03:52:47", "modified": "2021-04-11 04:20:23", "commits": 7 } ], "_score": 4, "_indexed": true, "_nocasepkg": "hummingbird", "_universes": [ "bioc", "eleniadam" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.23.0", "date": "2026-05-30T08:01:06.000Z", "distro": "noble", "arch": "aarch64", "commit": "80fd0db252348953091ea66ce0947c75a8c61656", "fileid": "bc6c33febec163a585b0a4a1e6a3a1af7fc491df88ce24c50b67cb7d0ec53b2e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678589748" }, { "r": "4.7.0", "os": "linux", "version": "1.23.0", "date": "2026-05-30T08:02:11.000Z", "distro": "noble", "arch": "x86_64", "commit": "80fd0db252348953091ea66ce0947c75a8c61656", "fileid": "47c0a63ac8a03888a8c0e4c27300b180865efbc9d3150738c739a13cfb13c6cb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678589748" }, { "r": "4.6.0", "os": "linux", "version": "1.23.0", "date": "2026-05-30T08:01:27.000Z", "distro": "noble", "arch": "aarch64", "commit": "80fd0db252348953091ea66ce0947c75a8c61656", "fileid": "0c628c775880e23448c470418489edf83efe2987d5df6f44e4b0f1fbed2ef116", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678589748" }, { "r": "4.6.0", "os": "linux", "version": "1.23.0", "date": "2026-05-30T08:02:00.000Z", "distro": "noble", "arch": "x86_64", "commit": "80fd0db252348953091ea66ce0947c75a8c61656", "fileid": "a679ad38a7f8744c442596d71c92b417b3188aed75f02d4c7c928c7ee4447d2c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678589748" }, { "r": "4.5.3", "os": "mac", "version": "1.23.0", "date": "2026-05-30T11:31:27.000Z", "arch": "aarch64", "commit": "80fd0db252348953091ea66ce0947c75a8c61656", "fileid": "dcc53587485ec69e7d7fdc69b004552a7db20bc48e6fa3f7214871e2aa96625a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678589748" }, { "r": "4.5.3", "os": "mac", "version": "1.23.0", "date": "2026-05-30T08:03:59.000Z", "arch": "x86_64", "commit": "80fd0db252348953091ea66ce0947c75a8c61656", "fileid": "98c3b416ab5e56f1b2200d73b8a88c1c4f817136043709555d6fcb28e306cc46", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678589748" }, { "r": "4.6.0", "os": "mac", "version": "1.23.0", "date": "2026-05-30T11:31:12.000Z", "arch": "aarch64", "commit": "80fd0db252348953091ea66ce0947c75a8c61656", "fileid": "29c79cccdba25c0063c92376cda8737799c49b92061e5d607cc6b86990f2d560", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678589748" }, { "r": "4.6.0", "os": "mac", "version": "1.23.0", "date": "2026-05-30T08:02:34.000Z", "arch": "x86_64", "commit": "80fd0db252348953091ea66ce0947c75a8c61656", "fileid": "7b8ec676a5a672b8513b8e03d6b9bc8a43bfe57c1ba115c51d10a78f65c3a3ee", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678589748" }, { "r": "4.6.0", "os": "wasm", "version": "1.23.0", "date": "2026-05-30T08:00:54.000Z", "arch": "emscripten", "commit": "80fd0db252348953091ea66ce0947c75a8c61656", "fileid": "ffc8f81d30d350ed179bc17f950268156844a11bd99d93712f3c1383bf3df38a", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678589748" }, { "r": "4.7.0", "os": "win", "version": "1.23.0", "date": "2026-05-30T08:00:16.000Z", "arch": "x86_64", "commit": "80fd0db252348953091ea66ce0947c75a8c61656", "fileid": "7eac31ba03720f609cae6a2c63f3be812f36a0b6ad5ca2e25fb451fcc502c353", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678589748" }, { "r": "4.5.3", "os": "win", "version": "1.23.0", "date": "2026-05-30T08:00:05.000Z", "arch": "x86_64", "commit": "80fd0db252348953091ea66ce0947c75a8c61656", "fileid": "898982b1f43ad6e3dbd8fe7ac7664d077a12c3bd16576a57664459a5abf48c42", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678589748" }, { "r": "4.6.0", "os": "win", "version": "1.23.0", "date": "2026-05-30T08:00:20.000Z", "arch": "x86_64", "commit": "80fd0db252348953091ea66ce0947c75a8c61656", "fileid": "08a88800a389e7b63d65da4a860dfbe2530438372636221da9ce575a74c8988f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678589748" } ] }