{ "_id": "6ae051464d02104fb3ec01b5", "Package": "divergence", "Title": "Divergence: Functionality for assessing omics data by divergence\nwith respect to a baseline", "Version": "1.29.0", "Author": "Wikum Dinalankara , Luigi Marchionni\n, Qian Ke ", "Maintainer": "Wikum Dinalankara , Luigi\nMarchionni ", "Description": "This package provides functionality for performing\ndivergence analysis as presented in Dinalankara et al,\n\"Digitizing omics profiles by divergence from a baseline\", PANS\n2018. This allows the user to simplify high dimensional omics\ndata into a binary or ternary format which encapsulates how the\ndata is divergent from a specified baseline group with the same\nunivariate or multivariate features.", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "6.1.1", "biocViews": "Software, StatisticalMethod", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:49:30 UTC", "RemoteUrl": "https://github.com/bioc/divergence", "RemoteRef": "HEAD", "RemoteSha": "51938bf679bba56f3f43b7c161d428429bdbce3a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-27 07:16:16 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "divergence_1.29.0.tar.gz", "_fileid": "https://r2.ropensci.org/80557991c168d324b27e8b8bbdfd26796bc82d3c24686eec342f763ddbceaeb2", "_filesize": 2300096, "_sha256": "80557991c168d324b27e8b8bbdfd26796bc82d3c24686eec342f763ddbceaeb2", "_expires": "2027-02-04T07:22:44.000Z", "_created": "2026-10-27T07:16:16.000Z", "_published": "2026-10-27T07:22:45.965Z", "_upstream": "https://github.com/bioc/divergence", "_status": "success", "_maintainer": { "name": "Wikum Dinalankara", "email": "marchion@jhu.edu" }, "_jobs": [ { "job": 122062002813, "time": 136, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "12716374593" }, { "job": 122062002755, "time": 335, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12717130549" }, { "job": 122062002840, "time": 299, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12716742155" }, { "job": 122062002828, "time": 224, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "12716741946" }, { "job": 122062002750, "time": 195, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "12716414888" }, { "job": 122059820684, "time": 389, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12716671506" }, { "job": 122062002890, "time": 96, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12716473844" }, { "job": 122062002880, "time": 206, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12716697053" }, { "job": 122062002783, "time": 196, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "12716871149" }, { "job": 122062002834, "time": 185, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12717030598" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 16 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/40465477426", "_commit": { "id": "51938bf679bba56f3f43b7c161d428429bdbce3a", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380570 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.29.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.28.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "software", "statisticalmethod" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 479, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 460, "source": "https://www.bioconductor.org/packages/stats/bioc/divergence" }, "_searchresults": 15, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/divergence.html", "extra/manual.pdf", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "computeChiSquaredTest", "computeMultivariateBinaryMatrix", "computeMultivariateDigitization", "computeMultivariateSupport", "computeQuantileMatrix", "computeUnivariateDigitization", "computeUnivariateSupport", "computeUnivariateTernaryMatrix", "findMultivariateGammaWithSupport", "findUnivariateGammaWithSupport" ], "_datasets": [ { "name": "breastTCGA_ER", "title": "ER positive or negative status of breast tumor samples", "object": "breastTCGA_ER", "class": [ "factor" ], "fields": [], "table": false, "tojson": true }, { "name": "breastTCGA_Group", "title": "Normal or Tumor status of breast samples", "object": "breastTCGA_Group", "class": [ "factor" ], "fields": [], "table": false, "tojson": true }, { "name": "breastTCGA_Mat", "title": "Gene expression for 260 genes in 887 breast samples", "object": "breastTCGA_Mat", "class": [ "matrix", "array" ], "fields": [], "rows": 260, "table": true, "tojson": true }, { "name": "msigdb_Hallmarks", "title": "Cancer Hallmark gene sets from the MSigDB collection", "object": "msigdb_Hallmarks", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "breastTCGA_ER", "title": "ER positive or negative status of breast tumor samples", "topics": [ "breastTCGA_ER" ] }, { "page": "breastTCGA_Group", "title": "Normal or Tumor status of breast samples", "topics": [ "breastTCGA_Group" ] }, { "page": "breastTCGA_Mat", "title": "Gene expression for 260 genes in 887 breast samples", "topics": [ "breastTCGA_Mat" ] }, { "page": "computeChiSquaredTest", "title": "Compute chi-squared test", "topics": [ "computeChiSquaredTest" ] }, { "page": "computeMultivariateBinaryMatrix", "title": "Compute the binary matrix with digitized divergence coding", "topics": [ "computeMultivariateBinaryMatrix" ] }, { "page": "computeMultivariateDigitization", "title": "Perform binary digitization", "topics": [ "computeMultivariateDigitization" ] }, { "page": "computeMultivariateSupport", "title": "Estimate the baseline support", "topics": [ "computeMultivariateSupport" ] }, { "page": "computeQuantileMatrix", "title": "Compute quantile transformations", "topics": [ "computeQuantileMatrix" ] }, { "page": "computeUnivariateDigitization", "title": "Perform ternary digitization", "topics": [ "computeUnivariateDigitization" ] }, { "page": "computeUnivariateSupport", "title": "Estimate the baseline support", "topics": [ "computeUnivariateSupport" ] }, { "page": "computeUnivariateTernaryMatrix", "title": "Compute the ternary matrix with digitized divergence coding", "topics": [ "computeUnivariateTernaryMatrix" ] }, { "page": "findMultivariateGammaWithSupport", "title": "Find optimal gamma and corresponding support for list of feature sets", "topics": [ "findMultivariateGammaWithSupport" ] }, { "page": "findUnivariateGammaWithSupport", "title": "Search for optimal gamma and associated support", "topics": [ "findUnivariateGammaWithSupport" ] }, { "page": "msigdb_Hallmarks", "title": "Cancer Hallmark gene sets from the MSigDB collection", "topics": [ "msigdb_Hallmarks" ] } ], "_readme": "https://github.com/bioc/divergence/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "DelayedArray", "generics", "GenomicRanges", "IRanges", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "S4Arrays", "S4Vectors", "Seqinfo", "SparseArray", "SummarizedExperiment", "XVector" ], "_vignettes": [ { "source": "divergence.Rmd", "filename": "divergence.html", "title": "Performing Divergence Analysis", "author": "Wikum Dinalankara, Luigi Marchionni, Qian Ke", "engine": "knitr", "headings": [], "created": "2019-01-04 13:29:04", "modified": "2019-02-15 15:42:32", "commits": 8 } ], "_score": 4.176091259055681, "_indexed": true, "_nocasepkg": "divergence", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.29.0", "date": "2026-10-27T07:20:16.000Z", "distro": "resolute", "commit": "51938bf679bba56f3f43b7c161d428429bdbce3a", "fileid": "https://r2.ropensci.org/44c9d2e74d8a424d10236505b14f70ba715cc359b4827270936695eee5c21d7b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40465477426" }, { "r": "4.6.1", "os": "linux", "version": "1.29.0", "date": "2026-10-27T07:20:13.000Z", "distro": "resolute", "commit": "51938bf679bba56f3f43b7c161d428429bdbce3a", "fileid": "https://r2.ropensci.org/630e20c91299a07dc54fa391c2af254a3bdf9ca94d7923d3d7f63925fb99b5dd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40465477426" }, { "r": "4.5.3", "os": "mac", "version": "1.29.0", "date": "2026-10-27T07:18:24.000Z", "commit": "51938bf679bba56f3f43b7c161d428429bdbce3a", "fileid": "https://r2.ropensci.org/10538118222fafeadfbfd8bb48db8febbeac67b46edcc0b4bc3367c21696920d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40465477426" }, { "r": "4.6.1", "os": "mac", "version": "1.29.0", "date": "2026-10-27T07:18:04.000Z", "commit": "51938bf679bba56f3f43b7c161d428429bdbce3a", "fileid": "https://r2.ropensci.org/a7ce8a213f119ec74bf5bf67e988df0501044081155a87d51ace4475f9298142", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40465477426" }, { "r": "4.6.0", "os": "wasm", "version": "1.29.0", "date": "2026-10-27T07:18:22.000Z", "commit": "51938bf679bba56f3f43b7c161d428429bdbce3a", "fileid": "https://r2.ropensci.org/b09769928a18677e6dbcc8f7bb9f326f3bef6de29d4936571856477844a71e74", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40465477426" }, { "r": "4.7.0", "os": "win", "version": "1.29.0", "date": "2026-10-27T07:17:42.000Z", "commit": "51938bf679bba56f3f43b7c161d428429bdbce3a", "fileid": "https://r2.ropensci.org/5d04483c8cba3d19f222bac664fac20561e0aaf617623119a08ae2193f1d90a6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40465477426" }, { "r": "4.5.3", "os": "win", "version": "1.29.0", "date": "2026-10-27T07:17:44.000Z", "commit": "51938bf679bba56f3f43b7c161d428429bdbce3a", "fileid": "https://r2.ropensci.org/b59812a579d2b247b325b0100a8bc979038cbf4977616c0c3238f3b799dfca7f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40465477426" }, { "r": "4.6.1", "os": "win", "version": "1.29.0", "date": "2026-10-27T07:17:42.000Z", "commit": "51938bf679bba56f3f43b7c161d428429bdbce3a", "fileid": "https://r2.ropensci.org/a893256b6634e4a5e53aadbb8e7ff84d6538d558186e4e89257e9affb504555f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/40465477426" } ] }