{ "_id": "6a1ad1fb1d7bb097a09e2ba6", "Package": "eudysbiome", "Type": "Package", "Title": "Cartesian plot and contingency test on 16S Microbial data", "Version": "1.43.0", "Date": "2016-05-19", "Author": "Xiaoyuan Zhou, Christine Nardini", "Maintainer": "Xiaoyuan Zhou ", "Description": "eudysbiome a package that permits to annotate the\ndifferential genera as harmful/harmless based on their ability\nto contribute to host diseases (as indicated in literature) or\nunknown based on their ambiguous genus classification. Further,\nthe package statistically measures the eubiotic (harmless\ngenera increase or harmful genera decrease) or\ndysbiotic(harmless genera decrease or harmful genera increase)\nimpact of a given treatment or environmental change on the\n(gut-intestinal, GI) microbiome in comparison to the microbiome\nof the reference condition.", "License": "GPL-2", "LazyData": "TRUE", "RoxygenNote": "5.0.1", "Config/pak/sysreqs": "libbz2-dev liblzma-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:41:38 UTC", "RemoteUrl": "https://github.com/bioc/eudysbiome", "RemoteRef": "HEAD", "RemoteSha": "33f2ad51027edbe009911cffd312386398a2368c", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:30:52 UTC", "User": "root" }, "MD5sum": "f8c32a8e360ac69dad4784b3859f18fd", "_user": "bioc", "_type": "src", "_file": "eudysbiome_1.43.0.tar.gz", "_fileid": "bbabacf72dc29eb7f18d739ffbe18e2f1cfa296ca80f7fb2824f529ce396e391", "_filesize": 4539699, "_sha256": "bbabacf72dc29eb7f18d739ffbe18e2f1cfa296ca80f7fb2824f529ce396e391", "_created": "2026-05-30T08:30:52.000Z", "_published": "2026-05-30T12:03:07.600Z", "_jobs": [ { "job": 78636730311, "time": 145, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306857402" }, { "job": 78636730328, "time": 197, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306862520" }, { "job": 78636730322, "time": 233, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306865863" }, { "job": 78636730317, "time": 172, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308029435" }, { "job": 78636730321, "time": 173, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308028697" }, { "job": 78636556003, "time": 199, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306842819" }, { "job": 78636730310, "time": 132, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306856153" }, { "job": 78636730324, "time": 133, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306856326" }, { "job": 78636730325, "time": 177, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306860411" }, { "job": 78636730330, "time": 104, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306853415" } ], "_bioccheck": { "error": 2, "warning": 2, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679228278", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/eudysbiome", "_commit": { "id": "33f2ad51027edbe009911cffd312386398a2368c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380098 }, "_maintainer": { "name": "Xiaoyuan Zhou", "email": "zhouxiaoyuan@picb.ac.cn" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.1.0", "role": "Depends" }, { "package": "plyr", "role": "Imports" }, { "package": "Rsamtools", "role": "Imports" }, { "package": "R.utils", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.43.0", "bioc": "3.24" }, { "branch": "release", "version": "1.42.0", "bioc": "3.23" } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 443, "source": "https://www.bioconductor.org/packages/stats/bioc/eudysbiome" }, "_mentions": 2, "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/eudysbiome.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "assignTax", "Cartesian", "contingencyCount", "contingencyTest", "microAnnotate", "tableSpecies" ], "_datasets": [ { "name": "diffGenera", "title": "Differential microbes in Genus-Species table A data frame containing 10 differential genera and the species included, which was to be annotated as '\"harmful\"' or '\"harmless\"'.", "object": "diffGenera", "class": [ "data.frame" ], "fields": [ "Genus", "Species" ], "rows": 26, "table": true, "tojson": true }, { "name": "harmGenera", "title": "Manually curated genera annotation table A data frame containing 260 genera annotated as \"harmful\" and the harmful species included in these genera.", "object": "harmGenera", "class": [ "data.frame" ], "fields": [ "Genus", "Species", "Ref." ], "rows": 900, "table": true, "tojson": true }, { "name": "microCount", "title": "Microbial count contingency table", "object": "microCount", "class": [ "matrix", "array" ], "fields": [ "EI", "DI" ], "rows": 3, "table": true, "tojson": true }, { "name": "microDiff", "title": "Differential annotated genera with abundance variations among pair-wise condition comparisons", "object": "microDiff", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "assignTax", "title": "Taxonomic Classification", "topics": [ "assignTax" ] }, { "page": "Cartesian", "title": "2-D Cartesian plane Plots", "topics": [ "Cartesian" ] }, { "page": "contingencyCount", "title": "Contingency Table Construction", "topics": [ "contingencyCount" ] }, { "page": "contingencyTest", "title": "Contingency test for count data", "topics": [ "contingencyTest" ] }, { "page": "diffGenera", "title": "Differential microbes in Genus-Species table A data frame containing 10 differential genera and the species included, which was to be annotated as '\"harmful\"' or '\"harmless\"'.", "topics": [ "diffGenera" ] }, { "page": "eudysbiome", "title": "eudysbiome.", "topics": [ "eudysbiome-package", "eudysbiome" ] }, { "page": "harmGenera", "title": "Manually curated genera annotation table A data frame containing 260 genera annotated as \"harmful\" and the harmful species included in these genera.", "topics": [ "harmGenera" ] }, { "page": "microAnnotate", "title": "Genus Annotation", "topics": [ "microAnnotate" ] }, { "page": "microCount", "title": "Microbial count contingency table", "topics": [ "microCount" ] }, { "page": "microDiff", "title": "Differential annotated genera with abundance variations among pair-wise condition comparisons", "topics": [ "microDiff" ] }, { "page": "tableSpecies", "title": "Construct a Genus-Species Data Frame", "topics": [ "tableSpecies" ] } ], "_rundeps": [ "BH", "BiocGenerics", "BiocParallel", "Biostrings", "bitops", "codetools", "cpp11", "crayon", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "IRanges", "lambda.r", "plyr", "R.methodsS3", "R.oo", "R.utils", "Rcpp", "Rhtslib", "Rsamtools", "S4Vectors", "Seqinfo", "snow", "XVector" ], "_vignettes": [ { "source": "eudysbiome.Rnw", "filename": "eudysbiome.pdf", "title": "eudysbiome User Manual", "engine": "utils::Sweave", "headings": [], "created": "2015-08-06 17:36:37", "modified": "2016-06-02 14:35:35", "commits": 3 } ], "_score": 3.6020599913279625, "_indexed": true, "_nocasepkg": "eudysbiome", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.43.0", "date": "2026-05-30T08:33:27.000Z", "distro": "noble", "commit": "33f2ad51027edbe009911cffd312386398a2368c", "fileid": "a9817f3bde6fdc22620de8ab5af8c6445804949ae02c7362c2225bf93f76022d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679228278" }, { "r": "4.6.0", "os": "linux", "version": "1.43.0", "date": "2026-05-30T08:34:08.000Z", "distro": "noble", "commit": "33f2ad51027edbe009911cffd312386398a2368c", "fileid": "00f1ce74e1074494e2a1b40b41d87acd2cf97b962767bfdd573a5e006076cb25", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679228278" }, { "r": "4.5.3", "os": "mac", "version": "1.43.0", "date": "2026-05-30T12:01:49.000Z", "commit": "33f2ad51027edbe009911cffd312386398a2368c", "fileid": "ecb65ab9febd5b2b5ffbbe30b6c832b276fb245b5e2b932b1e65b58cc5e2a0e9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679228278" }, { "r": "4.6.0", "os": "mac", "version": "1.43.0", "date": "2026-05-30T12:01:34.000Z", "commit": "33f2ad51027edbe009911cffd312386398a2368c", "fileid": "e5edbc9e75ded09a7a6f38fa0f1a0ae2dbbfba1521b9584e9a2283db22373d4a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679228278" }, { "r": "4.6.0", "os": "wasm", "version": "1.43.0", "date": "2026-05-30T08:33:23.000Z", "commit": "33f2ad51027edbe009911cffd312386398a2368c", "fileid": "ae334d1d4447a9ee3229b7ad340018d232aa9a53dce6910a095b9c9fcbfda531", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679228278" }, { "r": "4.7.0", "os": "win", "version": "1.43.0", "date": "2026-05-30T08:32:24.000Z", "commit": "33f2ad51027edbe009911cffd312386398a2368c", "fileid": "7aa62b0cb5bcc70ed8ce90c53fa5c50feecf3103085bbe44b0048a0376191f42", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679228278" }, { "r": "4.5.3", "os": "win", "version": "1.43.0", "date": "2026-05-30T08:33:06.000Z", "commit": "33f2ad51027edbe009911cffd312386398a2368c", "fileid": "2a45c240063e584dba321e334e1c81d00492a890ac380a5b4521dee1fa6daf4d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679228278" }, { "r": "4.6.0", "os": "win", "version": "1.43.0", "date": "2026-05-30T08:32:12.000Z", "commit": "33f2ad51027edbe009911cffd312386398a2368c", "fileid": "a072a75bc73a5c2d1c818ba90df7cdfff3327f686186e5d775e5c492380a819b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679228278" } ] }