{ "_id": "6acf48f4d9de2f3f33fca1fe", "Package": "mExplorer", "Version": "1.0.0", "License": "GPL (>= 2)", "Description": "The method 'm:Explorer' associates a given list of target\ngenes (e.g. those involved in a biological process) to gene\nregulators such as transcription factors. Transcription factors\nthat bind DNA near significantly many target genes or correlate\nwith target genes in transcriptional (microarray or RNAseq\ndata) are selected. Selection of candidate master regulators is\ncarried out using multinomial regression models, likelihood\nratio tests and multiple testing correction. Reference:\nm:Explorer: multinomial regression models reveal positive and\nnegative regulators of longevity in yeast quiescence. Juri\nReimand, Anu Aun, Jaak Vilo, Juan M Vaquerizas, Juhan Sedman\nand Nicholas M Luscombe. Genome Biology (2012) 13:R55\n.", "Title": "Identifying Master Gene Regulators from Gene Expression and\nDNA-Binding Data", "Authors@R": "person(\"Juri\", \"Reimand\", email = \"juri.reimand@utoronto.ca\", role = c(\"aut\", \"cre\"))", "Collate": "'mExplorer.R'", "NeedsCompilation": "no", "RoxygenNote": "6.0.1.9000", "Packaged": { "Date": "2026-10-14 08:24:04 UTC", "User": "root" }, "Author": "Juri Reimand [aut, cre]", "Maintainer": "Juri Reimand ", "Config/pak/sysreqs": "libfftw3-dev", "Repository": "https://reimand0.r-universe.dev", "Date/Publication": "2017-08-24 13:51:44 UTC", "RemoteUrl": "https://github.com/cran/mExplorer", "RemoteRef": "HEAD", "RemoteSha": "c9c122bd2f0bbdf5dc589c7b77a7b514dbf785b1", "_user": "reimand0", "_type": "src", "_file": "mExplorer_1.0.0.tar.gz", "_fileid": "https://r2.ropensci.org/2a1677329fc4fc0f0259f5bb8974780a6bcf5a94e79cf7b8199e5af851bc4c58", "_filesize": 130633, "_sha256": "2a1677329fc4fc0f0259f5bb8974780a6bcf5a94e79cf7b8199e5af851bc4c58", "_expires": "2027-01-22T09:18:42.000Z", "_created": "2026-10-14T08:24:04.000Z", "_published": "2026-10-14T09:18:44.765Z", "_buildurl": "https://github.com/r-universe/reimand0/actions/runs/38534473242", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 115755219261, "time": 97, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11879102944" }, { "job": 115755219383, "time": 92, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11879682893" }, { "job": 115755219198, "time": 100, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11882751546" }, { "job": 115755219304, "time": 114, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11881579772" }, { "job": 115754045187, "time": 181, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11878884093" }, { "job": 115755219369, "time": 89, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11879633351" }, { "job": 115755219394, "time": 71, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11879697983" }, { "job": 115755219337, "time": 60, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11879618326" }, { "job": 115755219404, "time": 61, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11879067979" } ], "_upstream": "https://github.com/cran/mExplorer", "_commit": { "id": "c9c122bd2f0bbdf5dc589c7b77a7b514dbf785b1", "author": "Juri Reimand ", "committer": "cran-robot ", "message": "version 1.0.0\n", "time": 1503582704 }, "_maintainer": { "name": "Juri Reimand", "email": "juri.reimand@utoronto.ca", "login": "reimand0", "description": "", "uuid": 19268349 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "nnet", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "qusage", "role": "Imports" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "reimand0", "count": 1, "uuid": 19268349 } ], "_userbio": { "uuid": 19268349, "type": "user", "name": "reimand0", "followers": 0 }, "_downloads": { "count": 267, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/mExplorer" }, "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/mExplorer.html" ], "_realowner": "reimand0", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2017-08-24" } ], "_exports": [ "mExplorer", "prepare_gmt_input" ], "_datasets": [ { "name": "small_test_dframe", "title": "Small sample of predictor data for testing m:Explorer", "object": "mExplorer_small_test_data", "file": "mExplorer_small_test_data.RData", "class": [ "data.frame" ], "fields": [ "mcm1", "mbp1", "ndd1", "swi4", "swi5", "swi6", "fkh1", "fkh2", "ace2", "rap1", "msn2", "hog1", "tup1", "ste12", "cup2", "ada2", "hsf1", "gal3" ], "rows": 10, "table": true, "tojson": true }, { "name": "small_test_response_vec", "title": "Small vector of yeast transcription factors for testing m:Explorer", "object": "mExplorer_small_test_data", "file": "mExplorer_small_test_data.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "yeastCCgenes", "title": "Example vector of yeast transcription factors for m:Explorer", "object": "yeastCCgenes", "file": "yeastCCgenes.RData", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "yeastTFdata", "title": "Example predictor data for m:Explorer", "object": "yeastTFdata", "file": "yeastTFdata.RData", "class": [ "data.frame" ], "fields": [ "mcm1", "mbp1", "ndd1", "swi4", "swi5", "swi6", "fkh1", "fkh2", "ace2", "rap1", "msn2", "hog1", "tup1", "ste12", "cup2", "ada2", "hsf1", "gal3" ], "rows": 6253, "table": true, "tojson": true } ], "_help": [ { "page": "mExplorer", "title": "Selection of process-specific regulators from high-throughput data using multinomial regression models.", "topics": [ "mExplorer" ] }, { "page": "prepare_gmt_input", "title": "Creation of m:Explorer input data frame from GMT files", "topics": [ "prepare_gmt_input" ] }, { "page": "small_test_dframe", "title": "Small sample of predictor data for testing m:Explorer", "topics": [ "small_test_dframe" ] }, { "page": "small_test_response_vec", "title": "Small vector of yeast transcription factors for testing m:Explorer", "topics": [ "small_test_response_vec" ] }, { "page": "yeastCCgenes", "title": "Example vector of yeast transcription factors for m:Explorer", "topics": [ "yeastCCgenes" ] }, { "page": "yeastTFdata", "title": "Example predictor data for m:Explorer", "topics": [ "yeastTFdata" ] } ], "_rundeps": [ "Biobase", "BiocGenerics", "emmeans", "estimability", "fftw", "generics", "lattice", "limma", "mvtnorm", "nlme", "nnet", "numDeriv", "qusage", "rlang", "statmod" ], "_score": 1, "_indexed": true, "_nocasepkg": "mexplorer", "_universes": [ "reimand0" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-10-14T08:25:51.000Z", "distro": "resolute", "commit": "c9c122bd2f0bbdf5dc589c7b77a7b514dbf785b1", "fileid": "https://r2.ropensci.org/897a97e38ca9bba6a395a8d1d2a5049385f7976402f6bc285e9447082e60afe4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/reimand0/actions/runs/38534473242" }, { "r": "4.6.1", "os": "linux", "version": "1.0.0", "date": "2026-10-14T08:25:48.000Z", "distro": "resolute", "commit": "c9c122bd2f0bbdf5dc589c7b77a7b514dbf785b1", "fileid": "https://r2.ropensci.org/4b3e1e825ac8268d56df439b8f415206f8b3fc74c117682fb5971102a0398495", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/reimand0/actions/runs/38534473242" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-10-14T09:17:20.000Z", "commit": "c9c122bd2f0bbdf5dc589c7b77a7b514dbf785b1", "fileid": "https://r2.ropensci.org/f67066ab0b7b64b6c67f0b30ada7c0714b783cfe369acceaae401d25e928a5b3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/reimand0/actions/runs/38534473242" }, { "r": "4.6.1", "os": "mac", "version": "1.0.0", "date": "2026-10-14T09:18:10.000Z", "commit": "c9c122bd2f0bbdf5dc589c7b77a7b514dbf785b1", "fileid": "https://r2.ropensci.org/ec9297a65d5b4ed4c67fa19a8dc0feb25a732906e4843f1a73a8b1628f695c91", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/reimand0/actions/runs/38534473242" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-10-14T08:25:56.000Z", "commit": "c9c122bd2f0bbdf5dc589c7b77a7b514dbf785b1", "fileid": "https://r2.ropensci.org/19c7940c163253bc6aff17fb7ce82c6a0d0e73e3ff74e1b34df2e53bf99bd8a6", "status": "success", "buildurl": "https://github.com/r-universe/reimand0/actions/runs/38534473242" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-10-14T08:25:19.000Z", "commit": "c9c122bd2f0bbdf5dc589c7b77a7b514dbf785b1", "fileid": "https://r2.ropensci.org/7d2ce64a839a07f4bfbb5d16fc7d9198cf008e22597fa738387ea736d210a4fe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/reimand0/actions/runs/38534473242" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-10-14T08:25:12.000Z", "commit": "c9c122bd2f0bbdf5dc589c7b77a7b514dbf785b1", "fileid": "https://r2.ropensci.org/f65082f98ebc585545280dc05c32bec79aca1868abf14d3fc4e331f21561df3f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/reimand0/actions/runs/38534473242" }, { "r": "4.6.1", "os": "win", "version": "1.0.0", "date": "2026-10-14T08:25:14.000Z", "commit": "c9c122bd2f0bbdf5dc589c7b77a7b514dbf785b1", "fileid": "https://r2.ropensci.org/ab94300c570b728e9df1e3cda80927e355c1fcd8f3562d4a721677d5694f4812", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/reimand0/actions/runs/38534473242" } ] }