{ "_id": "6a4941be18cdde069385e1e0", "Package": "clusterSeq", "Type": "Package", "Title": "Clustering of high-throughput sequencing data by identifying\nco-expression patterns", "Version": "1.37.0", "Date": "2016-01-19", "Authors@R": "c(person(\"Thomas J.\", \"Hardcastle\", role = \"aut\"),\nperson(\"Irene\", \"Papatheodorou\", role = \"aut\"),\nperson(\"Samuel\", \"Granjeaud\", role = \"cre\", email = \"samuel.granjeaud@inserm.fr\", comment=c(ORCID=\"0000-0001-9245-1535\")))", "Description": "Identification of clusters of co-expressed genes based on\ntheir expression across multiple (replicated) biological\nsamples.", "License": "GPL-3", "LazyLoad": "yes", "biocViews": "Sequencing, DifferentialExpression, MultipleComparison,\nClustering, GeneExpression", "URL": "https://github.com/samgg/clusterSeq", "BugReports": "https://github.com/samgg/clusterSeq/issues", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:44:49 UTC", "RemoteUrl": "https://github.com/bioc/clusterSeq", "RemoteRef": "HEAD", "RemoteSha": "39dc31c1a6b1f972eee95418cb1166bd8c44aea4", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 08:46:08 UTC", "User": "root" }, "Author": "Thomas J. Hardcastle [aut],\nIrene Papatheodorou [aut],\nSamuel Granjeaud [cre] (ORCID: )", "Maintainer": "Samuel Granjeaud ", "_user": "bioc", "_type": "src", "_file": "clusterSeq_1.37.0.tar.gz", "_fileid": "https://r2.ropensci.org/c7a02b321c71a2f5a5ebb487bcf6b64e40d684d9f60df88df5fb1bfa84eb4e81", "_filesize": 1175859, "_sha256": "c7a02b321c71a2f5a5ebb487bcf6b64e40d684d9f60df88df5fb1bfa84eb4e81", "_expires": "2026-10-12T17:24:12.000Z", "_created": "2026-07-04T08:46:08.000Z", "_published": "2026-07-04T17:24:14.345Z", "_bioccheck": { "error": 0, "warning": 1, "note": 11 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28700848367", "_status": "success", "_upstream": "https://github.com/bioc/clusterSeq", "_commit": { "id": "39dc31c1a6b1f972eee95418cb1166bd8c44aea4", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380289 }, "_maintainer": { "name": "Samuel Granjeaud", "email": "samuel.granjeaud@inserm.fr", "login": "samgg", "description": "first dot last at inserm dot fr", "uuid": 3333348, "orcid": "0000-0001-9245-1535" }, "_distro": "resolute", "_jobs": [ { "job": 85151943879, "time": 158, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8080176983" }, { "job": 85151943801, "time": 380, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8080201822" }, { "job": 85151943793, "time": 384, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8080202262" }, { "job": 85151943992, "time": 258, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8080438967" }, { "job": 85151943895, "time": 246, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8080437646" }, { "job": 85151943589, "time": 259, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8080159885" }, { "job": 85151943748, "time": 127, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8080173684" }, { "job": 85151943790, "time": 394, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8080203202" }, { "job": 85151943786, "time": 429, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8080207249" }, { "job": 85151943987, "time": 298, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8080192596" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "BiocParallel", "role": "Depends" }, { "package": "baySeq", "role": "Depends" }, { "package": "graphics", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "utils", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "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": "1.37.0", "bioc": "3.24" }, { "branch": "release", "version": "1.36.0", "bioc": "3.23" } ], "_topics": [ "sequencing", "differentialexpression", "multiplecomparison", "clustering", "geneexpression" ], "_stars": 0, "_contributors": [ { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 6, "uuid": 1744257 }, { "user": "samgg", "count": 4, "uuid": 3333348 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "lshep", "count": 2, "uuid": 18724380 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "link-ny", "count": 1, "uuid": 4392950 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/samgg/clusterseq", "_searchresults": 2, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/clusterSeq.html", "extra/contents.json", "manual.pdf" ], "_homeurl": "https://github.com/samgg/clusterseq", "_realowner": "bioc", "_cranurl": false, "_exports": [ "associatePosteriors", "kCluster", "makeClusters", "makeClustersFF", "plotCluster", "wallace" ], "_datasets": [ { "name": "cD.ratThymus", "title": "Data from female rat thymus tissue taken from the Rat BodyMap project (Yu et al, 2014) and processed by baySeq.", "object": "cD.ratThymus", "file": "cD.ratThymus.RData", "class": [ "countData" ], "fields": [], "table": false, "tojson": false }, { "name": "ratThymus", "title": "Data from female rat thymus tissue taken from the Rat BodyMap project (Yu et al, 2014).", "object": "ratThymus", "file": "ratThymus.RData", "class": [ "matrix", "array" ], "fields": [ "SEQC_Thm_F_002_1", "SEQC_Thm_F_002_2", "SEQC_Thm_F_002_3", "SEQC_Thm_F_002_4", "SEQC_Thm_F_006_1", "SEQC_Thm_F_006_2", "SEQC_Thm_F_006_3", "SEQC_Thm_F_006_4", "SEQC_Thm_F_021_1", "SEQC_Thm_F_021_2", "SEQC_Thm_F_021_3", "SEQC_Thm_F_021_4", "SEQC_Thm_F_104_1", "SEQC_Thm_F_104_2", "SEQC_Thm_F_104_3", "SEQC_Thm_F_104_4" ], "rows": 17230, "table": true, "tojson": true } ], "_help": [ { "page": "clusterSeq-package", "title": "Clustering of high-throughput sequencing data by identifying co-expression patterns", "topics": [ "clusterSeq-package", "clusterSeq" ] }, { "page": "associatePosteriors", "title": "Associates posterior likelihood to generate co-expression dissimilarities between genes", "topics": [ "associatePosteriors" ] }, { "page": "cD.ratThymus-data", "title": "Data from female rat thymus tissue taken from the Rat BodyMap project (Yu et al, 2014) and processed by baySeq.", "topics": [ "cD.ratThymus" ] }, { "page": "kCluster", "title": "Constructs co-expression dissimilarities from k-means analyses.", "topics": [ "kCluster" ] }, { "page": "makeClusters", "title": "Creates clusters from a co-expression minimal linkage data.frame.", "topics": [ "makeClusters" ] }, { "page": "makeClustersFF", "title": "Creates clusters from a file containing a full dissimilarity matrix.", "topics": [ "makeClustersFF" ] }, { "page": "plotCluster", "title": "Plots data from clusterings.", "topics": [ "plotCluster" ] }, { "page": "ratThymus-data", "title": "Data from female rat thymus tissue taken from the Rat BodyMap project (Yu et al, 2014).", "topics": [ "ratThymus" ] }, { "page": "wallace", "title": "Computes Wallace scores comparing two clustering methods.", "topics": [ "wallace" ] } ], "_rundeps": [ "abind", "baySeq", "BH", "BiocGenerics", "BiocParallel", "codetools", "cpp11", "edgeR", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "IRanges", "lambda.r", "lattice", "limma", "locfit", "S4Vectors", "Seqinfo", "snow", "statmod" ], "_vignettes": [ { "source": "clusterSeq.Rnw", "filename": "clusterSeq.pdf", "title": "Advanced baySeq analyses", "engine": "utils::Sweave", "headings": [ "1 Introduction", "2 K-means based clustering", "3 Posterior likelihood analyses" ], "created": "2016-12-12 22:17:22", "modified": "2018-08-30 17:46:18", "commits": 3 } ], "_score": 4.079181246047625, "_indexed": true, "_nocasepkg": "clusterseq", "_universes": [ "bioc", "samgg" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.37.0", "date": "2026-07-04T08:49:28.000Z", "distro": "resolute", "commit": "39dc31c1a6b1f972eee95418cb1166bd8c44aea4", "fileid": "https://r2.ropensci.org/980b63e64c13543687566a9eeafda7b996108b8d7cc7fff22ffb67b6ee115c63", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700848367" }, { "r": "4.6.1", "os": "linux", "version": "1.37.0", "date": "2026-07-04T08:49:37.000Z", "distro": "resolute", "commit": "39dc31c1a6b1f972eee95418cb1166bd8c44aea4", "fileid": "https://r2.ropensci.org/faf4c134860f039298985680fbe942b55b76101fc8668f12f59627907e564a26", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700848367" }, { "r": "4.5.3", "os": "mac", "version": "1.37.0", "date": "2026-07-04T09:22:47.000Z", "commit": "39dc31c1a6b1f972eee95418cb1166bd8c44aea4", "fileid": "https://r2.ropensci.org/a318fe562a1dd4007dee4b6f47d71fe9d4a0b81209500523274e4d9b065f7087", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700848367" }, { "r": "4.6.1", "os": "mac", "version": "1.37.0", "date": "2026-07-04T09:22:47.000Z", "commit": "39dc31c1a6b1f972eee95418cb1166bd8c44aea4", "fileid": "https://r2.ropensci.org/54d93da233764ed2c2163e81770f8c3952f52ea2eeae48ce5b9fe940382f481f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700848367" }, { "r": "4.6.0", "os": "wasm", "version": "1.37.0", "date": "2026-07-04T08:48:34.000Z", "commit": "39dc31c1a6b1f972eee95418cb1166bd8c44aea4", "fileid": "https://r2.ropensci.org/dd798a0720bc915eb227aa67591cf39cce223acb933702390099a865f83c4a5c", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700848367" }, { "r": "4.7.0", "os": "win", "version": "1.37.0", "date": "2026-07-04T08:47:41.000Z", "commit": "39dc31c1a6b1f972eee95418cb1166bd8c44aea4", "fileid": "https://r2.ropensci.org/b5eca30d7c8b8353e437668118855f8f0fe8f74f07698e4b043e7d5eb89e1f8a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700848367" }, { "r": "4.5.3", "os": "win", "version": "1.37.0", "date": "2026-07-04T08:47:44.000Z", "commit": "39dc31c1a6b1f972eee95418cb1166bd8c44aea4", "fileid": "https://r2.ropensci.org/9325d24a3992f28676d938b980941f1a1b2dc5380df06a6185500e88159e45d5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700848367" }, { "r": "4.6.1", "os": "win", "version": "1.37.0", "date": "2026-07-04T08:48:11.000Z", "commit": "39dc31c1a6b1f972eee95418cb1166bd8c44aea4", "fileid": "https://r2.ropensci.org/f229535ac60f292c11fcdfc7f8c3a4a6cf2900dc2e87a0ababa2474661246f33", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28700848367" } ] }