{ "_id": "6a195a5eacfb0bcc41de3f12", "Package": "mitch", "Title": "Multi-Contrast Gene Set Enrichment Analysis", "Version": "1.24.0", "Authors@R": "c(\nperson(given = \"Mark\",\nfamily = \"Ziemann\",\nrole = c(\"aut\",\"cre\",\"cph\"),\nemail = \"mark.ziemann@gmail.com\",\ncomment = c(ORCID=\"0000-0002-7688-6974\")),\nperson(given=\"Antony\",\nfamily=\"Kaspi\",\nrole = c(\"aut\",\"cph\"))\n)", "Description": "mitch is an R package for multi-contrast enrichment\nanalysis. At it’s heart, it uses a rank-MANOVA based\nstatistical approach to detect sets of genes that exhibit\nenrichment in the multidimensional space as compared to the\nbackground. The rank-MANOVA concept dates to work by Cox and\nMann (https://doi.org/10.1186/1471-2105-13-S16-S12). mitch is\nuseful for pathway analysis of profiling studies with one, two\nor more contrasts, or in studies with multiple omics profiling,\nfor example proteomic, transcriptomic, epigenomic analysis of\nthe same samples. mitch is perfectly suited for pathway level\ndifferential analysis of scRNA-seq data. We have an established\nroutine for pathway enrichment of Infinium Methylation Array\ndata (see vignette). The main strengths of mitch are that it\ncan import datasets easily from many upstream tools and has\nadvanced plotting features to visualise these enrichments.", "License": "CC BY-SA 4.0 + file LICENSE", "Encoding": "UTF-8", "URL": "https://github.com/markziemann/mitch", "BugReports": "https://github.com/markziemann/mitch", "LazyData": "false", "RoxygenNote": "7.3.2", "biocViews": "GeneExpression, GeneSetEnrichment, SingleCell,\nTranscriptomics, Epigenetics, Proteomics,\nDifferentialExpression, Reactome, DNAMethylation,\nMethylationArray, DataImport", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev make libharfbuzz-dev libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:51:28 UTC", "RemoteUrl": "https://github.com/bioc/mitch", "RemoteRef": "RELEASE_3_23", "RemoteSha": "1235d245813f65223c42062fedfae4404cccd6df", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:56:42 UTC", "User": "root" }, "Author": "Mark Ziemann [aut, cre, cph] (ORCID:\n),\nAntony Kaspi [aut, cph]", "Maintainer": "Mark Ziemann ", "MD5sum": "87f18bfe0b94d14ec2c3899292075dc3", "_user": "bioc-release", "_type": "src", "_file": "mitch_1.24.0.tar.gz", "_fileid": "4eb70c49979be13da70d52da597ea2e13ecc6660b3bb31ef30ea44221751d031", "_filesize": 1426461, "_sha256": "4eb70c49979be13da70d52da597ea2e13ecc6660b3bb31ef30ea44221751d031", "_created": "2026-05-29T07:56:42.000Z", "_published": "2026-05-29T09:20:30.368Z", "_jobs": [ { "job": 78461124661, "time": 416, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7286002102" }, { "job": 78461124636, "time": 560, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7286041661" }, { "job": 78461124647, "time": 568, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7286043872" }, { "job": 78461124646, "time": 379, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7287355144" }, { "job": 78461124645, "time": 368, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7287347045" }, { "job": 78459755343, "time": 591, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285885628" }, { "job": 78461124692, "time": 349, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285982739" }, { "job": 78461124765, "time": 1908, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7286430743" }, { "job": 78461124709, "time": 1909, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7286431106" }, { "job": 78461124788, "time": 1964, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7286449593" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 10 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625064734", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/mitch", "_commit": { "id": "1235d245813f65223c42062fedfae4404cccd6df", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380688 }, "_maintainer": { "name": "Mark Ziemann", "email": "mark.ziemann@gmail.com", "login": "markziemann", "mastodon": "@mdziemann@genomic.social", "orcid": "0000-0002-7688-6974", "description": "", "uuid": 5591840 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "GGally", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "knitr", "role": "Imports" }, { "package": "rmarkdown", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "beeswarm", "role": "Imports" }, { "package": "echarts4r", "role": "Imports" }, { "package": "kableExtra", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "network", "role": "Imports" }, { "package": "stringi", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" }, { "package": "HGNChelper", "role": "Suggests" }, { "package": "IlluminaHumanMethylation450kanno.ilmn12.hg19", "role": "Suggests" }, { "package": "IlluminaHumanMethylationEPICanno.ilm10b4.hg19", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-02", "n": 3 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23" } ], "_topics": [ "geneexpression", "genesetenrichment", "singlecell", "transcriptomics", "epigenetics", "proteomics", "differentialexpression", "reactome", "dnamethylation", "methylationarray", "dataimport", "gene-regulation", "gene-seq-analysis", "pathway-analysis" ], "_stars": 17, "_contributors": [ { "user": "markziemann", "count": 95, "uuid": 5591840 }, { "user": "jwokaty", "count": 14, "uuid": 1744257 }, { "user": "nturaga", "count": 10, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 357, "source": "https://www.bioconductor.org/packages/stats/bioc/mitch" }, "_mentions": 3, "_devurl": "https://github.com/markziemann/mitch", "_searchresults": 18, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/mitch.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/markziemann/mitch", "_realowner": "bioc", "_cranurl": false, "_exports": [ "gmt_import", "mitch_calc", "mitch_import", "mitch_plots", "mitch_report", "network_genes", "networkplot" ], "_datasets": [ { "name": "genesetsExample", "title": "Reactome gene sets", "object": "genesetsExample", "file": "genesetsExample.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "k36a", "title": "H3K36ac profile", "object": "k36a", "file": "k36a.RData", "class": [ "data.frame" ], "fields": [ "logFC", "logCPM", "PValue", "adj.p.value" ], "rows": 1000, "table": true, "tojson": true }, { "name": "k9a", "title": "H3K9ac profile", "object": "k9a", "file": "k9a.RData", "class": [ "data.frame" ], "fields": [ "logFC", "logCPM", "PValue", "adj.p.value" ], "rows": 1000, "table": true, "tojson": true }, { "name": "myImportedData", "title": "myImportedData: Example imported profiles", "object": "myImportedData", "file": "myImportedData.RData", "class": [ "data.frame" ], "fields": [ "rna", "k9a", "k36a" ], "rows": 1000, "table": true, "tojson": true }, { "name": "myList", "title": "myList: A list of three edgeR results", "object": "myList", "file": "myList.RData", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "resExample", "title": "resExample: Example mitch result", "object": "resExample", "file": "resExample.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "rna", "title": "RNA profile", "object": "rna", "file": "rna.RData", "class": [ "data.frame" ], "fields": [ "logFC", "logCPM", "PValue", "adj.p.value" ], "rows": 1000, "table": true, "tojson": true } ], "_help": [ { "page": "genesetsExample", "title": "Reactome gene sets", "topics": [ "genesetsExample" ] }, { "page": "gmt_import", "title": "gmt_import", "topics": [ "gmt_import" ] }, { "page": "k36a", "title": "H3K36ac profile", "topics": [ "k36a" ] }, { "page": "k9a", "title": "H3K9ac profile", "topics": [ "k9a" ] }, { "page": "mitch", "title": "mitch: An R package for multi-dimensional pathway enrichment analysis", "topics": [ "mitch-package", "mitch" ] }, { "page": "mitch_calc", "title": "mitch_calc", "topics": [ "mitch_calc" ] }, { "page": "mitch_import", "title": "mitch_import", "topics": [ "mitch_import" ] }, { "page": "mitch_plots", "title": "mitch_plots", "topics": [ "mitch_plots" ] }, { "page": "mitch_report", "title": "mitch_report", "topics": [ "mitch_report" ] }, { "page": "myImportedData", "title": "myImportedData: Example imported profiles", "topics": [ "myImportedData" ] }, { "page": "myList", "title": "myList: A list of three edgeR results", "topics": [ "myList" ] }, { "page": "network_genes", "title": "network_genes", "topics": [ "network_genes" ] }, { "page": "networkplot", "title": "networkplot", "topics": [ "networkplot" ] }, { "page": "resExample", "title": "resExample: Example mitch result", "topics": [ "resExample" ] }, { "page": "rna", "title": "RNA profile", "topics": [ "rna" ] } ], "_readme": "https://github.com/bioc/mitch/raw/RELEASE_3_23/README.md", "_rundeps": [ "backports", "base64enc", "beeswarm", "bitops", "broom", "bslib", "cachem", "caTools", "cli", "coda", "commonmark", "corrplot", "countrycode", "cpp11", "crayon", "digest", "dplyr", "echarts4r", "evaluate", "farver", "fastmap", "fontawesome", "forcats", "fs", "generics", "GGally", "ggplot2", "ggstats", "glue", "gplots", "gridExtra", "gtable", "gtools", "highr", "hms", "htmltools", "htmlwidgets", "httpuv", "isoband", "jquerylib", "jsonlite", "kableExtra", "KernSmooth", "knitr", "labeling", "later", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "memoise", "mime", "network", "otel", "patchwork", "pillar", "pkgconfig", "plyr", "prettyunits", "progress", "promises", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "rlang", "rmarkdown", "rstudioapi", "S7", "sass", "scales", "shiny", "sourcetools", "statnet.common", "stringi", "stringr", "svglite", "systemfonts", "textshaping", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "withr", "xfun", "xml2", "xtable", "yaml" ], "_vignettes": [ { "source": "infiniumMethArrayWorkflow.Rmd", "filename": "infiniumMethArrayWorkflow.html", "title": "Applying mitch to pathway analysis of Infinium Methylation array data", "author": "Antony Kaspi & Mark Ziemann", "engine": "knitr::rmarkdown", "headings": [ "Background", "Requirements", "Gene sets", "Probe gene relationship for HM450K array data", "Update deprecated gene symbols", "Importing profiling data", "Calculating enrichment", "Downstream presentation", "Probe gene relationship for EPIC array data", "Session Info" ], "created": "2024-02-19 02:49:43", "modified": "2025-03-31 14:45:17", "commits": 4 }, { "source": "mitchWorkflow.Rmd", "filename": "mitchWorkflow.html", "title": "mitch Workflow", "author": "Antony Kaspi & Mark Ziemann", "engine": "knitr::rmarkdown", "headings": [ "Background", "Importing gene sets", "Importing profiling data", "Calculating enrichment", "Generate a HTML report", "Generate high resolution plots", "Network plot", "Session Info" ], "created": "2019-10-06 23:42:29", "modified": "2025-03-31 14:45:17", "commits": 10 } ], "_score": 6.564902672529205, "_indexed": false, "_nocasepkg": "mitch", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/mitch", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.24.0", "date": "2026-05-29T08:03:19.000Z", "distro": "noble", "commit": "1235d245813f65223c42062fedfae4404cccd6df", "fileid": "97cb08da63f2fa295a62cf197d63015dac2226cdb555c7e8e4939ee3535e9ac1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625064734" }, { "r": "4.6.0", "os": "linux", "version": "1.24.0", "date": "2026-05-29T08:03:34.000Z", "distro": "noble", "commit": "1235d245813f65223c42062fedfae4404cccd6df", "fileid": "b4d43be9cbbc92c27f551734a45e5d6ed74d873fbf744e70c50bfffd4361af00", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625064734" }, { "r": "4.5.3", "os": "mac", "version": "1.24.0", "date": "2026-05-29T09:17:47.000Z", "commit": "1235d245813f65223c42062fedfae4404cccd6df", "fileid": "58cbb71f6bcce0c8bda72b8b0aa745111641192bf76296cedfaf9cd78373c627", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625064734" }, { "r": "4.6.0", "os": "mac", "version": "1.24.0", "date": "2026-05-29T09:17:36.000Z", "commit": "1235d245813f65223c42062fedfae4404cccd6df", "fileid": "02717ef11544b9b521a49aefc57365fb61f5f4624989dd963de27b7f5dcca7c2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625064734" }, { "r": "4.6.0", "os": "wasm", "version": "1.24.0", "date": "2026-05-29T08:02:48.000Z", "commit": "1235d245813f65223c42062fedfae4404cccd6df", "fileid": "5bd9c22cb5a587ee3439ecc97d33c132208f7520cb566138fd119871d2b95fee", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625064734" }, { "r": "4.7.0", "os": "win", "version": "1.24.0", "date": "2026-05-29T08:25:06.000Z", "commit": "1235d245813f65223c42062fedfae4404cccd6df", "fileid": "730c06698b3c2dd5c993392a98ec0e8db0b5023694f2c6900274862fcfbfcf67", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625064734" }, { "r": "4.5.3", "os": "win", "version": "1.24.0", "date": "2026-05-29T08:25:17.000Z", "commit": "1235d245813f65223c42062fedfae4404cccd6df", "fileid": "e9b49fc671ac6c4d55f6dde08ed6299a94c0be2e30189949f46961bdbfe9707f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625064734" }, { "r": "4.6.0", "os": "win", "version": "1.24.0", "date": "2026-05-29T08:26:15.000Z", "commit": "1235d245813f65223c42062fedfae4404cccd6df", "fileid": "f0f44d4336a56abf9bd139bc58107735e4ab0d96811c0afd1d58907421794b44", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26625064734" } ] }