{ "_id": "6a1c13ba1d7bb097a0a2f378", "Package": "OVESEG", "Type": "Package", "Title": "OVESEG-test to detect tissue/cell-specific markers", "Version": "1.29.0", "Author": "Lulu Chen ", "Maintainer": "Lulu Chen ", "biocViews": "Software, MultipleComparison, CellBiology, GeneExpression", "Description": "An R package for multiple-group comparison to detect\ntissue/cell-specific marker genes among subtypes. It provides\nfunctions to compute OVESEG-test statistics, derive component\nweights in the mixture null distribution model and estimate\np-values from weightedly aggregated permutations. Obtained\nposterior probabilities of component null hypotheses can also\nportrait all kinds of upregulation patterns among subtypes.", "License": "GPL-2", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "BugReports": "https://github.com/Lululuella/OVESEG", "RoxygenNote": "6.1.1", "SystemRequirements": "C++11", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:49:23 UTC", "RemoteUrl": "https://github.com/bioc/OVESEG", "RemoteRef": "HEAD", "RemoteSha": "45a3e56b444bd4b861ec9c2f1173378c815a02ca", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-31 10:49:36 UTC", "User": "root" }, "MD5sum": "85f1b626eb7c7f3187accdb9c6d664e4", "_user": "bioc", "_type": "src", "_file": "OVESEG_1.29.0.tar.gz", "_fileid": "95ed1f57aa8cb2543cdd089d9933353df0fd263d1e07c2e6df8765a9f0c87ed7", "_filesize": 791311, "_sha256": "95ed1f57aa8cb2543cdd089d9933353df0fd263d1e07c2e6df8765a9f0c87ed7", "_created": "2026-05-31T10:49:36.000Z", "_published": "2026-05-31T10:55:54.793Z", "_jobs": [ { "job": 78719895212, "time": 206, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7316120775" }, { "job": 78719895277, "time": 187, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7316118494" }, { "job": 78719895262, "time": 229, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7316123281" }, { "job": 78719895275, "time": 219, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7316122012" }, { "job": 78719895279, "time": 334, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7316134532" }, { "job": 78719895278, "time": 135, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7316112748" }, { "job": 78719895270, "time": 284, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7316129166" }, { "job": 78719895259, "time": 185, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7316118238" }, { "job": 78719895265, "time": 248, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7316125346" }, { "job": 78719351437, "time": 568, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7316098205" }, { "job": 78719895207, "time": 132, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7316112144" }, { "job": 78719895229, "time": 242, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7316124558" }, { "job": 78719895246, "time": 169, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7316116496" }, { "job": 78719895209, "time": 199, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7316120670" } ], "_bioccheck": { "error": 1, "warning": 0, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26710353734", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/OVESEG", "_commit": { "id": "45a3e56b444bd4b861ec9c2f1173378c815a02ca", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380563 }, "_maintainer": { "name": "Lulu Chen", "email": "luluchen@vt.edu" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "fdrtool", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" }, { "package": "grid", "role": "Suggests" }, { "package": "reshape2", "role": "Suggests" }, { "package": "scales", "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" }, { "branch": "release", "version": "1.28.0", "bioc": "3.23" } ], "_topics": [ "software", "multiplecomparison", "cellbiology", "geneexpression", "cpp" ], "_stars": 2, "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 352, "source": "https://www.bioconductor.org/packages/stats/bioc/OVESEG" }, "_devurl": "https://github.com/lululuella/oveseg", "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/OVESEG.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/lululuella/oveseg", "_realowner": "bioc", "_cranurl": false, "_exports": [ "nullDistri", "OVESEGtest", "OVESEGtstat", "OVEtstatPermTopM", "patternDistri", "postProbNull", "pvalueWeightedEst" ], "_datasets": [ { "name": "countBT", "title": "RNAseq count data downsampled from GSE60424", "object": "countBT", "file": "countBT.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "RocheBT", "title": "mRNA expression data downsampled from GSE28490 (Roche)", "object": "RocheBT", "file": "RocheBT.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "OVESEG-package", "title": "OVESEG: A package for marker gene test.", "topics": [ "OVESEG-package", "OVESEG" ] }, { "page": "countBT", "title": "RNAseq count data downsampled from GSE60424", "topics": [ "countBT" ] }, { "page": "nullDistri", "title": "Probability of one group being upregulated under null", "topics": [ "nullDistri" ] }, { "page": "OVESEGtest", "title": "OVESEG-test", "topics": [ "OVESEGtest" ] }, { "page": "OVESEGtstat", "title": "OVESEG-test statistics", "topics": [ "OVESEGtstat" ] }, { "page": "OVEtstatPermTopM", "title": "OVESEG-test statistics after permuting top M groups", "topics": [ "OVEtstatPermTopM" ] }, { "page": "patternDistri", "title": "Probabilities of all upregulation patterns", "topics": [ "patternDistri" ] }, { "page": "postProbNull", "title": "Posterior probabilities of each component null hypothesis", "topics": [ "postProbNull" ] }, { "page": "pvalueWeightedEst", "title": "p-value by weighted permutation scheme", "topics": [ "pvalueWeightedEst" ] }, { "page": "RocheBT", "title": "mRNA expression data downsampled from GSE28490 (Roche)", "topics": [ "RocheBT" ] } ], "_readme": "https://github.com/bioc/OVESEG/raw/HEAD/README.md", "_rundeps": [ "abind", "BH", "Biobase", "BiocGenerics", "BiocParallel", "codetools", "cpp11", "DelayedArray", "fdrtool", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "IRanges", "lambda.r", "lattice", "limma", "Matrix", "MatrixGenerics", "matrixStats", "Rcpp", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "statmod", "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": "OVESEG.Rmd", "filename": "OVESEG.html", "title": "OVESEG User Manual", "author": "Lulu Chen", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Quick Start", "OVESEG-test", "Datatypes and Input Format", "Microarray data", "RNAseq count data", "p-values", "Useful intermediate results", "Test statistics", "Posterior probabilities of null hypothesis components", "Notes", "sessionInfo", "References" ], "created": "2019-01-13 05:14:19", "modified": "2019-01-14 18:44:26", "commits": 3 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "oveseg", "_universes": [ "bioc", "lululuella" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.29.0", "date": "2026-05-31T10:52:23.000Z", "distro": "noble", "arch": "aarch64", "commit": "45a3e56b444bd4b861ec9c2f1173378c815a02ca", "fileid": "c2b31758ce0423eb7349ec137011c4216f37f5c1d25c78649c2b9be407233d7e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710353734" }, { "r": "4.7.0", "os": "linux", "version": "1.29.0", "date": "2026-05-31T10:52:59.000Z", "distro": "noble", "arch": "x86_64", "commit": "45a3e56b444bd4b861ec9c2f1173378c815a02ca", "fileid": "c52b8de8907665c9a11c7d837d9b9c51f019425f792b2e925581631c1b8eb6d8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710353734" }, { "r": "4.6.0", "os": "linux", "version": "1.29.0", "date": "2026-05-31T10:52:54.000Z", "distro": "noble", "arch": "aarch64", "commit": "45a3e56b444bd4b861ec9c2f1173378c815a02ca", "fileid": "8f72c9a348a7a613480846ebc02479f23d8f0c6fb01dfc5dcec22dda85f09825", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710353734" }, { "r": "4.6.0", "os": "linux", "version": "1.29.0", "date": "2026-05-31T10:54:50.000Z", "distro": "noble", "arch": "x86_64", "commit": "45a3e56b444bd4b861ec9c2f1173378c815a02ca", "fileid": "a1798e4a842d4592aa18a14e998f7636087045bb5ce950452e4562d0a8cb4608", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710353734" }, { "r": "4.5.3", "os": "mac", "version": "1.29.0", "date": "2026-05-31T10:51:33.000Z", "arch": "aarch64", "commit": "45a3e56b444bd4b861ec9c2f1173378c815a02ca", "fileid": "ba0b88b1dfb1a4f14854380e0080b777453b711e65cac684640d117408aedd60", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710353734" }, { "r": "4.5.3", "os": "mac", "version": "1.29.0", "date": "2026-05-31T10:53:26.000Z", "arch": "x86_64", "commit": "45a3e56b444bd4b861ec9c2f1173378c815a02ca", "fileid": "4296163927036a3a06e786a54ce990377df4d2b91997b5147c0899efc013f060", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710353734" }, { "r": "4.6.0", "os": "mac", "version": "1.29.0", "date": "2026-05-31T10:52:06.000Z", "arch": "aarch64", "commit": "45a3e56b444bd4b861ec9c2f1173378c815a02ca", "fileid": "6b5c49a61c1eaea72fd9b64fc48405ef2a6c062fea645c55809581c0bce786ca", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710353734" }, { "r": "4.6.0", "os": "mac", "version": "1.29.0", "date": "2026-05-31T10:52:55.000Z", "arch": "x86_64", "commit": "45a3e56b444bd4b861ec9c2f1173378c815a02ca", "fileid": "8c11ee2acca0fdce5b44a6dbd5da55d39f2e41bd203b65e9787d12637dfc6df0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710353734" }, { "r": "4.6.0", "os": "wasm", "version": "1.29.0", "date": "2026-05-31T10:52:13.000Z", "arch": "emscripten", "commit": "45a3e56b444bd4b861ec9c2f1173378c815a02ca", "fileid": "45a0f677fd79d9bf1dd9b8fd8aac8afdd282a877ffc5f79020af2dcb50d83615", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710353734" }, { "r": "4.7.0", "os": "win", "version": "1.29.0", "date": "2026-05-31T10:51:58.000Z", "arch": "x86_64", "commit": "45a3e56b444bd4b861ec9c2f1173378c815a02ca", "fileid": "fd749909dc6016759f19baa67211cad17310732ad10a7f29219bb253a42ae1c0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710353734" }, { "r": "4.5.3", "os": "win", "version": "1.29.0", "date": "2026-05-31T10:51:37.000Z", "arch": "x86_64", "commit": "45a3e56b444bd4b861ec9c2f1173378c815a02ca", "fileid": "00238f36128c12a3f00142b880dbf4d8fb7a56f14ecf770f5169b26f243a5d0b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710353734" }, { "r": "4.6.0", "os": "win", "version": "1.29.0", "date": "2026-05-31T10:51:56.000Z", "arch": "x86_64", "commit": "45a3e56b444bd4b861ec9c2f1173378c815a02ca", "fileid": "95084e975a39a468b492a7fa958249c7ac0accd01e9fcfcda56c80d3275a56ac", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26710353734" } ] }