{ "_id": "6a3aaea944e65c5976a8618b", "Package": "ROTS", "Type": "Package", "Title": "Reproducibility-Optimized Test Statistic", "Version": "2.5.1", "Author": "Fatemeh Seyednasrollah, Tomi Suomi, Laura L. Elo", "Maintainer": "Tomi Suomi ", "Description": "Calculates the Reproducibility-Optimized Test Statistic\n(ROTS) for differential testing in omics data.", "biocViews": "Software, GeneExpression, DifferentialExpression,\nMicroarray, RNASeq, Proteomics, ImmunoOncology", "License": "GPL (>= 2)", "LazyData": "yes", "NeedsCompilation": "yes", "Config/pak/sysreqs": "cmake make", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-30 13:40:19 UTC", "RemoteUrl": "https://github.com/bioc/ROTS", "RemoteRef": "HEAD", "RemoteSha": "cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99", "Packaged": { "Date": "2026-06-23 15:48:55 UTC", "User": "root" }, "MD5sum": "ff081eee4744ca41fb3d61207835a90e", "_user": "bioc", "_type": "src", "_file": "ROTS_2.5.1.tar.gz", "_fileid": "f0b8c8f8fbe8e0234acb3bd114f9bb04882c3895ad0311b97a56af1cdf6537f4", "_filesize": 479408, "_sha256": "f0b8c8f8fbe8e0234acb3bd114f9bb04882c3895ad0311b97a56af1cdf6537f4", "_created": "2026-06-23T15:48:55.000Z", "_published": "2026-06-23T16:04:57.682Z", "_jobs": [ { "job": 82997742312, "time": 178, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7826050341" }, { "job": 82997742435, "time": 199, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7826060862" }, { "job": 82997742424, "time": 259, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7826085605" }, { "job": 82997742428, "time": 199, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7826060308" }, { "job": 82997742441, "time": 258, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7826085521" }, { "job": 82997742395, "time": 214, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7826308141" }, { "job": 82997742418, "time": 355, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7826369822" }, { "job": 82997742475, "time": 164, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7826287879" }, { "job": 82997742443, "time": 210, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7826317764" }, { "job": 82996793066, "time": 254, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7825970366" }, { "job": 82997742245, "time": 133, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7826030826" }, { "job": 82997742566, "time": 167, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7826045116" }, { "job": 82997742286, "time": 178, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7826049836" }, { "job": 82997742372, "time": 215, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7826051172" } ], "_bioccheck": { "error": 2, "warning": 3, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28038062797", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/ROTS", "_commit": { "id": "cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99", "author": "Tomi Suomi ", "committer": "Tomi Suomi ", "message": "Bump version\n", "time": 1777556419 }, "_maintainer": { "name": "Tomi Suomi", "email": "tomi.suomi@utu.fi", "login": "suomtomi", "description": "", "uuid": 32176114 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "lme4", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 3, "_updates": [ { "week": "2025-28", "n": 4 }, { "week": "2025-44", "n": 2 }, { "week": "2025-48", "n": 3 }, { "week": "2025-49", "n": 1 }, { "week": "2025-50", "n": 1 }, { "week": "2026-04", "n": 4 }, { "week": "2026-06", "n": 2 }, { "week": "2026-17", "n": 1 }, { "week": "2026-18", "n": 3 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.5.1", "bioc": "3.24" }, { "branch": "release", "version": "2.4.0", "bioc": "3.23" } ], "_topics": [ "software", "geneexpression", "differentialexpression", "microarray", "rnaseq", "proteomics", "immunooncology", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 441, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 20, "_searchresults": 148, "_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/ROTS.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "coxphROTS", "lmeROTS", "lmROTS", "results", "ROTS" ], "_datasets": [ { "name": "affySpikeIn", "title": "Gene expression data from the Affymetrix spike-in experiment", "object": "affySpikeIn", "class": [ "matrix", "array" ], "fields": [ "X1521m99hpp.av06.CEL", "X1521n99hpp.av06.CEL", "X1521o99hpp.av06.CEL", "X1521p99hpp.av06.CEL", "X1532m99hpp.av04.CEL", "X1521q99hpp.av06.CEL", "X1521r99hpp.av06.CEL", "X1521s99hpp.av06.CEL", "X1521t99hpp.av06.CEL", "X1532q99hpp.av04.CEL" ], "rows": 1000, "table": true, "tojson": true }, { "name": "affySpikeIn.gnames", "title": "Gene expression data from the Affymetrix spike-in experiment", "object": "affySpikeIn", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "affySpikeIn.L", "title": "Gene expression data from the Affymetrix spike-in experiment", "object": "affySpikeIn", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "spikedgene", "title": "Gene expression data from the Affymetrix spike-in experiment", "object": "affySpikeIn", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "upsSpikeIn", "title": "Protein expression data from the CPTAC Technology Assessment (Study 6)", "object": "upsSpikeIn", "class": [ "data.frame" ], "fields": [ "A1", "A2", "A3", "C1", "C2", "C3" ], "rows": 736, "table": true, "tojson": true } ], "_help": [ { "page": "affySpikeIn", "title": "Gene expression data from the Affymetrix spike-in experiment", "topics": [ "affySpikeIn", "affySpikeIn.gnames", "affySpikeIn.L", "spikedgene" ] }, { "page": "coxphROTS", "title": "Reproducibility-Optimized Test Statistic (ROTS)", "topics": [ "coxphROTS" ] }, { "page": "lmeROTS", "title": "Reproducibility-Optimized Test Statistic (ROTS)", "topics": [ "lmeROTS" ] }, { "page": "lmROTS", "title": "Reproducibility-Optimized Test Statistic (ROTS)", "topics": [ "lmROTS" ] }, { "page": "plot.regROTS", "title": "Plotting of a regROTS object", "topics": [ "plot.regROTS" ] }, { "page": "plot.ROTS", "title": "Plotting of a ROTS object", "topics": [ "plot.ROTS" ] }, { "page": "results", "title": "Gathering results from a regROTS object", "topics": [ "results" ] }, { "page": "ROTS", "title": "Reproducibility-Optimized Test Statistic (ROTS)", "topics": [ "ROTS-package", "print.ROTS", "ROTS" ] }, { "page": "summary.regROTS", "title": "Summary of a regROTS object", "topics": [ "summary.regROTS" ] }, { "page": "summary.ROTS", "title": "Summary of a ROTS object", "topics": [ "summary.ROTS" ] }, { "page": "upsSpikeIn", "title": "Protein expression data from the CPTAC Technology Assessment (Study 6)", "topics": [ "upsSpikeIn" ] } ], "_rundeps": [ "BH", "Biobase", "BiocGenerics", "BiocParallel", "boot", "codetools", "cpp11", "formatR", "futile.logger", "futile.options", "generics", "lambda.r", "lattice", "lme4", "MASS", "Matrix", "minqa", "nlme", "nloptr", "rbibutils", "Rcpp", "RcppEigen", "Rdpack", "reformulas", "rlang", "snow", "survival" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "ROTS.Rnw", "filename": "ROTS.pdf", "title": "ROTS: Reproducibility Optimized Test Statistic", "engine": "utils::Sweave", "headings": [ "Introduction", "Algorithm overview", "Input data", "Preprocessing", "Differential expression testing", "Visualization", "References" ], "created": "2016-02-09 16:40:36", "modified": "2023-02-17 13:19:52", "commits": 6 } ], "_score": 7.078746734273608, "_indexed": true, "_nocasepkg": "rots", "_universes": [ "bioc", "suomtomi" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.5.1", "date": "2026-06-23T15:52:00.000Z", "distro": "resolute", "arch": "aarch64", "commit": "cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99", "fileid": "2bc8a993a35285120295905c2b590f68eb7552b5b07fb78f4ae7d31e92ad51a5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28038062797" }, { "r": "4.7.0", "os": "linux", "version": "2.5.1", "date": "2026-06-23T15:52:37.000Z", "distro": "resolute", "arch": "x86_64", "commit": "cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99", "fileid": "2de2317deab4b066ce9d887e2ba9b03bd98dea45214888a289d97b3d6dde2289", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28038062797" }, { "r": "4.6.0", "os": "linux", "version": "2.5.1", "date": "2026-06-23T15:52:00.000Z", "distro": "resolute", "arch": "aarch64", "commit": "cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99", "fileid": "f30bf1510af6b8e4e03c5fd7ba439c5569078137e5a6958133a409cb62dde16d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28038062797" }, { "r": "4.6.0", "os": "linux", "version": "2.5.1", "date": "2026-06-23T15:52:41.000Z", "distro": "resolute", "arch": "x86_64", "commit": "cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99", "fileid": "5e7219596c8e62f8d5b76181ffb78d190e841a9c042e2cc4a9f48bd880c6ecee", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28038062797" }, { "r": "4.5.3", "os": "mac", "version": "2.5.1", "date": "2026-06-23T16:00:56.000Z", "arch": "aarch64", "commit": "cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99", "fileid": "d4f30c4b161f5426c1e4717af05b0d97df94c5a0a7e2b8177eea456e2c041feb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28038062797" }, { "r": "4.5.3", "os": "mac", "version": "2.5.1", "date": "2026-06-23T16:02:18.000Z", "arch": "x86_64", "commit": "cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99", "fileid": "7876fbafafc636d2d8f645df35e39b41715eecaac59e96153c91a9b1bd3c5d60", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28038062797" }, { "r": "4.6.0", "os": "mac", "version": "2.5.1", "date": "2026-06-23T16:00:21.000Z", "arch": "aarch64", "commit": "cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99", "fileid": "d439b107cbaaec90e6baaf917072fce337ed073c6532156b41a096f1477c02d9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28038062797" }, { "r": "4.6.0", "os": "mac", "version": "2.5.1", "date": "2026-06-23T16:01:11.000Z", "arch": "x86_64", "commit": "cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99", "fileid": "8beec4e19f3a32e722470b0b8f3bb5bcb6d0c2b7b82f97372a906baf5c45aaff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28038062797" }, { "r": "4.6.0", "os": "wasm", "version": "2.5.1", "date": "2026-06-23T15:51:30.000Z", "arch": "emscripten", "commit": "cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99", "fileid": "db198009b3618c0f07873566e34ba22dbdb15ef37553f75f691ee604b01140ad", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28038062797" }, { "r": "4.7.0", "os": "win", "version": "2.5.1", "date": "2026-06-23T15:50:41.000Z", "arch": "x86_64", "commit": "cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99", "fileid": "5fa4db01251741c8c7f573785b2a37fa4613badcdac74dcfb0b622c3d54d0abb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28038062797" }, { "r": "4.5.3", "os": "win", "version": "2.5.1", "date": "2026-06-23T15:50:41.000Z", "arch": "x86_64", "commit": "cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99", "fileid": "20d598367fb74d15286faf629ee1ad369d8a0cb436268bbb9cccdf5c678bdded", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28038062797" }, { "r": "4.6.0", "os": "win", "version": "2.5.1", "date": "2026-06-23T15:50:41.000Z", "arch": "x86_64", "commit": "cce4fb43044ae1d90ef8e7a8ddb602cbad5e1c99", "fileid": "77b865dff795565c6ca29911b92f018700eea141971754710dc145c18083409d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28038062797" } ] }