{ "_id": "6a1060e5acfb0bcc41ca768e", "Package": "MiRSEA", "Type": "Package", "Version": "1.1", "Date": "2015-06-30", "Title": "'MicroRNA' Set Enrichment Analysis", "Author": "Junwei Han, Siyao Liu", "Maintainer": "Junwei Han ", "Description": "The tools for 'MicroRNA Set Enrichment Analysis' can\nidentify risk pathways(or prior gene sets) regulated by\nmicroRNA set in the context of microRNA expression data. (1)\nThis package constructs a correlation profile of microRNA and\npathways by the hypergeometric statistic test. The gene sets of\npathways derived from the three public databases (Kyoto\nEncyclopedia of Genes and Genomes ('KEGG'); 'Reactome';\n'Biocarta') and the target gene sets of microRNA are provided\nby four databases('TarBaseV6.0'; 'mir2Disease'; 'miRecords';\n'miRTarBase';). (2) This package can quantify the change of\ncorrelation between microRNA for each pathway(or prior gene\nset) based on a microRNA expression data with cases and\ncontrols. (3) This package uses the weighted Kolmogorov-Smirnov\nstatistic to calculate an enrichment score (ES) of a microRNA\nset that co-regulate to a pathway , which reflects the degree\nto which a given pathway is associated with the specific\nphenotype. (4) This package can provide the visualization of\nthe results.", "Collate": "Corrp2miRfile.R EnrichmentScore.R S2N.R MirSEA.R MsReport.R\nGetExampleData.R getEnvironmentData.R GetMiRTargetData.R\nGetPathwayData.R PlotCorrelation.R PlotHeatMap.R\nPlotRunEnrichment.R", "LazyData": "Yes", "License": "GPL (>= 2)", "biocViews": "Statistics, Pathways, microRNA, enrichment analysis", "Packaged": { "Date": "2026-05-08 08:21:56 UTC", "User": "root" }, "NeedsCompilation": "no", "Repository": "https://hanjunwei-lab.r-universe.dev", "Date/Publication": "2020-06-30 13:18:48 UTC", "RemoteUrl": "https://github.com/hanjunwei-lab/mirsea", "RemoteRef": "HEAD", "RemoteSha": "2914d2e41ba742589d80e91c0559cc3e83e3692b", "MD5sum": "e0d765b6594f690b4a87fef3a967af06", "_user": "hanjunwei-lab", "_type": "src", "_file": "MiRSEA_1.1.tar.gz", "_fileid": "74ffbfc334c2622cc3dcb83643ffbe80de8cae2f7e14fd46c93b25815a52c817", "_filesize": 1288000, "_sha256": "74ffbfc334c2622cc3dcb83643ffbe80de8cae2f7e14fd46c93b25815a52c817", "_created": "2026-05-08T08:21:56.000Z", "_published": "2026-05-22T13:57:57.418Z", "_distro": "noble", "_jobs": [ { "job": 77394411780, "time": 99, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "6874948899" }, { "job": 77394412114, "time": 102, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "6874948155" }, { "job": 77394411903, "time": 88, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "6874944320" }, { "job": 77394411949, "time": 66, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "6874938391" }, { "job": 77394411481, "time": 208, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6874919942" }, { "job": 77394411109, "time": 123, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7162290449" }, { "job": 77394411726, "time": 89, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "6874946199" }, { "job": 77394411891, "time": 97, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "6874946569" }, { "job": 77394411960, "time": 74, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "6874940290" } ], "_buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/25545088451", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/hanjunwei-lab/mirsea", "_commit": { "id": "2914d2e41ba742589d80e91c0559cc3e83e3692b", "author": "hanjunwei-lab ", "committer": "hanjunwei-lab ", "message": "update readme\n", "time": 1593523128 }, "_maintainer": { "name": "Junwei Han", "email": "hanjunwei1981@163.com", "login": "hanjunwei-lab", "uuid": 60877533 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.15.1", "role": "Depends" }, { "package": "stats", "role": "Suggests" }, { "package": "graphics", "role": "Suggests" }, { "package": "grDevices", "role": "Suggests" } ], "_owner": "hanjunwei-lab", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_topics": [ "statistics", "pathways", "microrna", "enrichment analysis" ], "_stars": 0, "_contributors": [ { "user": "hanjunwei-lab", "count": 4, "uuid": 60877533 } ], "_userbio": { "uuid": 60877533, "type": "user", "name": "Junwei Han", "description": "Junwei Han is a professor in Harbin Medical University. His research is in the areas of bioinformatics and computational systems biology." }, "_downloads": { "count": 212, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MiRSEA" }, "_mentions": 4, "_devurl": "https://github.com/hanjunwei-lab/mirsea", "_searchresults": 17, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MiRSEA.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/hanjunwei-lab/mirsea", "_realowner": "hanjunwei-lab", "_cranurl": true, "_releases": [ { "version": "1.0", "date": "2015-05-31" }, { "version": "1.1", "date": "2015-07-01" }, { "version": "1.1.1", "date": "2024-01-24" } ], "_exports": [ "Corrp2miRfile", "EnrichmentScore", "EnrichmentScore2", "Getenvir", "GetExampleData", "GetMiRTargetData", "GetPathwayData", "HeatMapPlot", "initializeMiRSEA", "MirSEA", "MsReport", "PlotCorrelation", "PlotHeatMap", "PlotRunEnrichment", "S2N" ], "_datasets": [ { "name": "envData", "title": "The variables in the environment include predefine pathway, target information of miRNAs,an expression profile and a example result of miRNA list", "object": "envData", "class": [ "environment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "MiRSEA-package", "title": "MicroRNA Set Enrichment Analysis", "topics": [ "MiRSEA-package", "MiRSEA" ] }, { "page": "Corrp2miRfile", "title": "create a pathway-microRNA(miRNA) profile and a p value matrix", "topics": [ "Corrp2miRfile" ] }, { "page": "EnrichmentScore", "title": "Computes the enrichment score", "topics": [ "EnrichmentScore" ] }, { "page": "EnrichmentScore2", "title": "Computes the enrichment score faster", "topics": [ "EnrichmentScore2" ] }, { "page": "envData", "title": "The variables in the environment include predefine pathway, target information of miRNAs,an expression profile and a example result of miRNA list", "topics": [ "envData", "example.cls", "example.gct", "mfile", "miRList", "p", "p2miR", "pathway" ] }, { "page": "GetExampleData", "title": "Get the example data", "topics": [ "GetExampleData" ] }, { "page": "GetMiRTargetData", "title": "Get the data of microRNA(miRNA) and target genes", "topics": [ "GetMiRTargetData" ] }, { "page": "GetPathwayData", "title": "Get the gene sets of pathways", "topics": [ "GetPathwayData" ] }, { "page": "HeatMapPlot", "title": "Plot a heatmap", "topics": [ "HeatMapPlot" ] }, { "page": "MirSEA", "title": "Identify dysregulated pathways based on microRNA (miRNA) set enrichment analysis", "topics": [ "MirSEA" ] }, { "page": "MsReport", "title": "Produce report for a microRNA (abbreviated miRNA) set", "topics": [ "MsReport" ] }, { "page": "PlotCorrelation", "title": "Plot global microRNA(miRNA) correlation profile", "topics": [ "PlotCorrelation" ] }, { "page": "PlotHeatMap", "title": "Plot a heat map", "topics": [ "PlotHeatMap" ] }, { "page": "PlotRunEnrichment", "title": "Plot running microRNAs(miRNAs) enrichment score", "topics": [ "PlotRunEnrichment" ] }, { "page": "S2N", "title": "calculate signal to noise ratio for microRNAs(miRNAs)", "topics": [ "S2N" ] } ], "_readme": "https://github.com/hanjunwei-lab/mirsea/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "MiRSEA.Rnw", "filename": "MiRSEA.pdf", "title": "MiRSEA Overview", "engine": "utils::Sweave", "headings": [], "created": "2020-06-27 10:38:03", "modified": "2020-06-27 10:38:03", "commits": 1 } ], "_score": 4.531478917042255, "_indexed": true, "_nocasepkg": "mirsea", "_universes": [ "hanjunwei-lab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1", "date": "2026-05-08T08:23:45.000Z", "distro": "noble", "commit": "2914d2e41ba742589d80e91c0559cc3e83e3692b", "fileid": "c4ee577461e40a0485e1b618015a4a0a0d7ed2d55f6400ac83bafd73af25c943", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/25545088451" }, { "r": "4.6.0", "os": "linux", "version": "1.1", "date": "2026-05-08T08:23:42.000Z", "distro": "noble", "commit": "2914d2e41ba742589d80e91c0559cc3e83e3692b", "fileid": "bb458d1ea3ecf52f0dfd40ad4c29606aa7d3fe043e3a3169a434c45eb4e8eaa9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/25545088451" }, { "r": "4.5.3", "os": "mac", "version": "1.1", "date": "2026-05-08T08:23:31.000Z", "commit": "2914d2e41ba742589d80e91c0559cc3e83e3692b", "fileid": "a6419d784406d9619c4024dc9c7fcc2d9dff41b8e43d3b5dda7ead61c7e07ba4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/25545088451" }, { "r": "4.6.0", "os": "mac", "version": "1.1", "date": "2026-05-08T08:23:10.000Z", "commit": "2914d2e41ba742589d80e91c0559cc3e83e3692b", "fileid": "f4e100eab2be196670e153361391a9e8aa1e666f6867da13ede4ff15d3c50f3a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/25545088451" }, { "r": "4.7.0", "os": "win", "version": "1.1", "date": "2026-05-08T08:23:32.000Z", "commit": "2914d2e41ba742589d80e91c0559cc3e83e3692b", "fileid": "899fcbd86b1d0b1c103a161ed1acbc57466187bc4589468b05164f515c50afe6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/25545088451" }, { "r": "4.5.3", "os": "win", "version": "1.1", "date": "2026-05-08T08:23:36.000Z", "commit": "2914d2e41ba742589d80e91c0559cc3e83e3692b", "fileid": "4901ea1338dbc148a59fc41c1501eb9f23acda730f16130f67e4f32f0f88d01a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/25545088451" }, { "r": "4.6.0", "os": "win", "version": "1.1", "date": "2026-05-08T08:23:08.000Z", "commit": "2914d2e41ba742589d80e91c0559cc3e83e3692b", "fileid": "1e40a28d097d55a0fc019b49556bf873a497d9af578ccf9a6ec04d7a32f1f95f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/25545088451" }, { "r": "4.6.0", "os": "wasm", "version": "1.1", "date": "2026-05-22T13:57:40.000Z", "commit": "2914d2e41ba742589d80e91c0559cc3e83e3692b", "fileid": "9965e5c6a1a118b12d205b5b906a7a448d99e8c58c61bc944fef33a7bb971cac", "status": "success", "buildurl": "https://github.com/r-universe/hanjunwei-lab/actions/runs/25545088451" } ] }