{ "_id": "6a493ec3a19c9318096e7d0c", "Package": "GeneExpressionSignature", "Title": "Gene Expression Signature based Similarity Metric", "Version": "1.59.0", "Date": "2012-12-16", "Authors@R": "c(person(given = \"Yang\",\nfamily = \"Cao\",\nrole = c(\"aut\", \"cre\"),\nemail = \"yiluheihei@gmail.com\"),\nperson(given = \"Fei\",\nfamily = \"Li\",\nrole = \"ctb\",\nemail = \"pittacus@gmail.com\"),\nperson(given = \"Lu\",\nfamily = \"Han\",\nrole = \"ctb\",\nemail = \"hanl8910@gmail.com\"))", "Description": "This package gives the implementations of the gene\nexpression signature and its distance to each. Gene expression\nsignature is represented as a list of genes whose expression is\ncorrelated with a biological state of interest. And its\ndistance is defined using a nonparametric, rank-based\npattern-matching strategy based on the Kolmogorov-Smirnov\nstatistic. Gene expression signature and its distance can be\nused to detect similarities among the signatures of drugs,\ndiseases, and biological states of interest.", "License": "GPL-2", "URL": "https://github.com/yiluheihei/GeneExpressionSignature", "BugReports": "https://github.com/yiluheihei/GeneExpressionSignature/issues/", "LazyLoad": "yes", "biocViews": "GeneExpression", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:35:43 UTC", "RemoteUrl": "https://github.com/bioc/GeneExpressionSignature", "RemoteRef": "HEAD", "RemoteSha": "dfa732bab5c071219ecff8a114273617be239ce5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 03:59:08 UTC", "User": "root" }, "Author": "Yang Cao [aut, cre],\nFei Li [ctb],\nLu Han [ctb]", "Maintainer": "Yang Cao ", "_user": "bioc", "_type": "src", "_file": "GeneExpressionSignature_1.59.0.tar.gz", "_fileid": "https://r2.ropensci.org/ac698ce8acd1fc2dd76eaf3a51772ff288aef2a05e09b58903069ce31b7f2cfc", "_filesize": 2554889, "_sha256": "ac698ce8acd1fc2dd76eaf3a51772ff288aef2a05e09b58903069ce31b7f2cfc", "_expires": "2026-10-12T17:11:29.000Z", "_created": "2026-07-04T03:59:08.000Z", "_published": "2026-07-04T17:11:31.129Z", "_bioccheck": { "error": 0, "warning": 1, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28694157939", "_status": "success", "_upstream": "https://github.com/bioc/GeneExpressionSignature", "_commit": { "id": "dfa732bab5c071219ecff8a114273617be239ce5", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379743 }, "_maintainer": { "name": "Yang Cao", "email": "yiluheihei@gmail.com", "login": "yiluheihei", "description": "R, Bioinformatics", "uuid": 6010251 }, "_distro": "resolute", "_jobs": [ { "job": 85151070983, "time": 156, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8078104996" }, { "job": 85151071209, "time": 223, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8078112133" }, { "job": 85151071213, "time": 167, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8078106270" }, { "job": 85151071079, "time": 90, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8078097206" }, { "job": 85151071199, "time": 102, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8078098635" }, { "job": 85151070938, "time": 198, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8078086874" }, { "job": 85151071096, "time": 160, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8078105380" }, { "job": 85151071039, "time": 90, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8078097210" }, { "job": 85151071164, "time": 85, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8078096577" }, { "job": 85151071052, "time": 106, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8078099247" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "Biobase", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "apcluster", "role": "Suggests" }, { "package": "GEOquery", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "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": "1.59.0", "bioc": "3.24" }, { "branch": "release", "version": "1.58.0", "bioc": "3.23" } ], "_topics": [ "geneexpression" ], "_stars": 1, "_contributors": [ { "user": "dtenenba", "count": 21, "uuid": 2286826 }, { "user": "nturaga", "count": 8, "uuid": 2746443 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "sonali-bioc", "count": 1, "uuid": 6373953 }, { "user": "yiluheihei", "count": 1, "uuid": 6010251 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 2, "_devurl": "https://github.com/yiluheihei/geneexpressionsignature", "_searchresults": 6, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GeneExpressionSignature.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/yiluheihei/geneexpressionsignature", "_realowner": "bioc", "_cranurl": false, "_exports": [ "getRLs", "RankMerging", "ScoreGSEA", "ScorePGSEA", "SignatureDistance" ], "_datasets": [ { "name": "exampleSet", "title": "sample data, a subset of the C-MAP", "object": "exampleSet", "file": "exampleSet.rda", "class": [ "ExpressionSet" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "exampleSet", "title": "sample data, a subset of the C-MAP", "topics": [ "exampleSet" ] }, { "page": "GeneExpressionSignature", "title": "Gene Expression Signature based Similarity Metric", "topics": [ "GeneExpressionSignature" ] }, { "page": "getRLs", "title": "Convert gene expression profiles to a ranked list", "topics": [ "getRLs" ] }, { "page": "RankMerging", "title": "Merging the ranker lists with the same labels of the biological states into a single list with the Iorio's method", "topics": [ "RankMerging" ] }, { "page": "ScoreGSEA", "title": "Compute pairwise distances between samples with method in package GSEA", "topics": [ "ScoreGSEA" ] }, { "page": "ScorePGSEA", "title": "Compute pairwise distances between samples with method in package PGSEA", "topics": [ "ScorePGSEA" ] }, { "page": "SignatureDistance", "title": "Compute pairwise distances comprehensively", "topics": [ "SignatureDistance" ] } ], "_readme": "https://github.com/bioc/GeneExpressionSignature/raw/HEAD/README.md", "_rundeps": [ "Biobase", "BiocGenerics", "generics" ], "_vignettes": [ { "source": "GeneExpressionSignature.Rmd", "filename": "GeneExpressionSignature.html", "title": "GeneExpressionSignature: Computing pairwise distances between different biological states", "author": "Yang Cao, Fei Li", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Getting Started", "Data Ranking", "Rank Merging", "Similarity Measuring", "Signature Distance", "Implementation Details", "Adaptively Weighted Rank Merging", "Eqully Weighted Rank Merging", "Futher Analysis", "Session Information", "References" ], "created": "2020-12-17 05:38:17", "modified": "2020-12-17 05:38:17", "commits": 1 } ], "_score": 5, "_indexed": true, "_nocasepkg": "geneexpressionsignature", "_universes": [ "bioc", "yiluheihei" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.59.0", "date": "2026-07-04T04:02:38.000Z", "distro": "resolute", "commit": "dfa732bab5c071219ecff8a114273617be239ce5", "fileid": "https://r2.ropensci.org/853631729e49b0d2a1e277773c5fc68fb2e3279222818bec367ccb700317ff1b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694157939" }, { "r": "4.6.1", "os": "linux", "version": "1.59.0", "date": "2026-07-04T04:01:43.000Z", "distro": "resolute", "commit": "dfa732bab5c071219ecff8a114273617be239ce5", "fileid": "https://r2.ropensci.org/9f6777f0af992dfe8d36b1c6ac789414c61acb1c5d0cd00baa964e9f43d7e259", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694157939" }, { "r": "4.5.3", "os": "mac", "version": "1.59.0", "date": "2026-07-04T04:00:38.000Z", "commit": "dfa732bab5c071219ecff8a114273617be239ce5", "fileid": "https://r2.ropensci.org/f04e7e54545b3f0fca1d12171b1a56694c93aaf3fcaba099ba0d865405898119", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694157939" }, { "r": "4.6.1", "os": "mac", "version": "1.59.0", "date": "2026-07-04T04:00:44.000Z", "commit": "dfa732bab5c071219ecff8a114273617be239ce5", "fileid": "https://r2.ropensci.org/60f472e7bd0f23ebacc4ef66594e55c70c3f9ad2bad22a351a786c7a759efd17", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694157939" }, { "r": "4.6.0", "os": "wasm", "version": "1.59.0", "date": "2026-07-04T04:02:02.000Z", "commit": "dfa732bab5c071219ecff8a114273617be239ce5", "fileid": "https://r2.ropensci.org/99c84173cdb532ed2bcd48aaa5c4a686607e2880b7208a6d2a2439fb9670e14a", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694157939" }, { "r": "4.7.0", "os": "win", "version": "1.59.0", "date": "2026-07-04T04:00:19.000Z", "commit": "dfa732bab5c071219ecff8a114273617be239ce5", "fileid": "https://r2.ropensci.org/b15e5286d8c245fc8b3d1dd01cb28ea66a4375cf720a436129729bc4727f87d3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694157939" }, { "r": "4.5.3", "os": "win", "version": "1.59.0", "date": "2026-07-04T04:00:18.000Z", "commit": "dfa732bab5c071219ecff8a114273617be239ce5", "fileid": "https://r2.ropensci.org/5d14b8743ab36af76eec620e38e34a20c2253ac05a10f865a462a99bff7a8203", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694157939" }, { "r": "4.6.1", "os": "win", "version": "1.59.0", "date": "2026-07-04T04:00:30.000Z", "commit": "dfa732bab5c071219ecff8a114273617be239ce5", "fileid": "https://r2.ropensci.org/a90d6a8c49c3dd441638f9680fbe418b2f166fb3851bcdb59d02382025fbab33", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28694157939" } ] }