{ "_id": "6a4b5025a6574ff277f996bd", "Package": "MKomics", "Version": "0.8", "Date": "2026-05-07", "Title": "Omics Data Analysis", "Authors@R": "person(\"Matthias\", \"Kohl\", role = c(\"aut\", \"cre\"),\nemail = \"Matthias.Kohl@stamats.de\",\ncomment = c(ORCID = \"0000-0001-9514-8910\"))", "Author": "Matthias Kohl [aut, cre] (0000-0001-9514-8910)", "Maintainer": "Matthias Kohl ", "VignetteBuilder": "knitr", "Description": "Similarity plots based on correlation and median absolute\ndeviation (MAD); adjusting colors for heatmaps; aggregate\ntechnical replicates; calculate pairwise fold-changes and log\nfold-changes; compute one- and two-way ANOVA; simplified\ninterface to package 'limma' (Ritchie et al. (2015),\n ) for moderated t-test and one-way\nANOVA; Hamming and Levenshtein (edit) distance of strings as\nwell as optimal alignment scores for global (Needleman-Wunsch)\nand local (Smith-Waterman) alignments with constant gap\npenalties (Merkl and Waack (2009), ISBN:978-3-527-32594-8).", "License": "LGPL-3", "URL": "https://www.stamats.de/", "Config/pak/sysreqs": "libpng-dev perl", "Repository": "https://stamats.r-universe.dev", "Date/Publication": "2026-05-07 16:27:42 UTC", "RemoteUrl": "https://github.com/stamats/mkomics", "RemoteRef": "HEAD", "RemoteSha": "799e9de1f4830d06f584674ddb1b3287e7c2b02a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-06 06:45:52 UTC", "User": "root" }, "_user": "stamats", "_type": "src", "_file": "MKomics_0.8.tar.gz", "_fileid": "https://r2.ropensci.org/03fd9bec93407e0466095d37c58ad0565f122acd9be2e8963e8631a3d6e01e13", "_filesize": 1034982, "_sha256": "03fd9bec93407e0466095d37c58ad0565f122acd9be2e8963e8631a3d6e01e13", "_expires": "2026-10-14T06:50:11.000Z", "_created": "2026-07-06T06:45:52.000Z", "_published": "2026-07-06T06:50:13.777Z", "_jobs": [ { "job": 85311035165, "time": 162, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8101606166" }, { "job": 85311035169, "time": 210, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8101619330" }, { "job": 85311035196, "time": 111, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8101613666" }, { "job": 85311035161, "time": 106, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8101605618" }, { "job": 85310580211, "time": 193, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8101560674" }, { "job": 85311035168, "time": 119, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8101594322" }, { "job": 85311035228, "time": 107, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8101591529" }, { "job": 85311035226, "time": 117, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8101593666" }, { "job": 85311035225, "time": 121, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8101595013" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/stamats/actions/runs/28772990297", "_status": "success", "_upstream": "https://github.com/stamats/mkomics", "_commit": { "id": "799e9de1f4830d06f584674ddb1b3287e7c2b02a", "author": "stamats ", "committer": "stamats ", "message": "updates for submission to CRAN\n", "time": 1778171262 }, "_maintainer": { "name": "Matthias Kohl", "email": "matthias.kohl@stamats.de", "login": "stamats", "orcid": "0000-0001-9514-8910", "description": "Professor of Mathematics in Biology and Medicine at Furtwangen University", "uuid": 11901280 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "robustbase", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "circlize", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "stamats", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-37", "n": 1 }, { "week": "2026-19", "n": 1 } ], "_tags": [], "_stars": 3, "_contributors": [ { "user": "stamats", "count": 46, "uuid": 11901280 } ], "_userbio": { "uuid": 11901280, "type": "user", "name": "Matthias Kohl", "followers": 36, "description": "Professor of Mathematics in Biology and Medicine at Furtwangen University" }, "_downloads": { "count": 279, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MKomics" }, "_devurl": "https://github.com/stamats/mkomics", "_searchresults": 51, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MKomics.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/stamats/mkomics", "_realowner": "stamats", "_cranurl": true, "_releases": [ { "version": "0.5", "date": "2020-02-19" }, { "version": "0.7", "date": "2021-08-08" }, { "version": "0.8", "date": "2026-05-07" } ], "_exports": [ "corDist", "corPlot", "corPlot2", "heatmapCol", "madMatrix", "madPlot", "madPlot2", "mod.oneway.test", "mod.t.test", "oneWayAnova", "pairwise.fc", "pairwise.logfc", "pairwise.mod.t.test", "repMeans", "simPlot", "simPlot2", "stringDist", "stringSim", "traceBack", "twoWayAnova" ], "_help": [ { "page": "0MKomics-package", "title": "Omics Data Analysis.", "topics": [ "MKomics-package", "MKomics" ] }, { "page": "corDist", "title": "Correlation Distance Matrix Computation", "topics": [ "corDist" ] }, { "page": "corPlot", "title": "Plot of similarity matrix based on correlation", "topics": [ "corPlot", "corPlot2" ] }, { "page": "heatmapCol", "title": "Generate colors for heatmaps", "topics": [ "heatmapCol" ] }, { "page": "madMatrix", "title": "Compute MAD between colums of a matrix or data.frame", "topics": [ "madMatrix" ] }, { "page": "madPlot", "title": "Plot of similarity matrix based on MAD", "topics": [ "madPlot", "madPlot2" ] }, { "page": "mod.oneway.test", "title": "Moderated 1-Way ANOVA", "topics": [ "mod.oneway.test" ] }, { "page": "mod.t.test", "title": "Moderated t-Test", "topics": [ "mod.t.test" ] }, { "page": "oneWayAnova", "title": "A function for Analysis of Variance", "topics": [ "oneWayAnova" ] }, { "page": "pairwiseFC", "title": "Compute pairwise fold changes", "topics": [ "pairwise.fc" ] }, { "page": "pairwiselogFC", "title": "Compute pairwise log-fold changes", "topics": [ "pairwise.logfc" ] }, { "page": "pairwise.mod.t.test", "title": "Pairwise Moderated t-Tests", "topics": [ "pairwise.mod.t.test" ] }, { "page": "repMeans", "title": "Compute mean of replicated spots", "topics": [ "repMeans" ] }, { "page": "simPlot", "title": "Plot of a similarity matrix.", "topics": [ "simPlot", "simPlot2" ] }, { "page": "stringDist", "title": "Function to compute distances between strings", "topics": [ "stringDist" ] }, { "page": "stringSim", "title": "Function to compute similarity scores between strings", "topics": [ "stringSim" ] }, { "page": "traceBack", "title": "Function to trace back", "topics": [ "traceBack" ] }, { "page": "twoWayAnova", "title": "A function for Analysis of Variance", "topics": [ "twoWayAnova" ] } ], "_readme": "https://github.com/stamats/mkomics/raw/HEAD/README.md", "_rundeps": [ "BiocGenerics", "circlize", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "crayon", "DEoptimR", "digest", "doParallel", "foreach", "generics", "GetoptLong", "GlobalOptions", "IRanges", "iterators", "limma", "matrixStats", "png", "RColorBrewer", "rjson", "robustbase", "S4Vectors", "shape", "statmod" ], "_vignettes": [ { "source": "MKomics.Rmd", "filename": "MKomics.html", "title": "Package MKomics", "author": "Matthias Kohl", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Moderated Tests Based on Package limma", "Moderated t-Test", "Moderated 1-Way ANOVA", "Pairwise moderated t-tests", "Pairwise Comparisons", "FC and logFC", "Aggregating Technical Replicates", "1- and 2-Way ANOVA", "Correlation Distance Matrix", "MAD Matrix", "Similarity Matrices", "Colors for Heatmaps", "String Alignment", "String Distances", "String Similarities", "Optimal Alignment", "sessionInfo", "References" ], "created": "2019-08-20 06:59:33", "modified": "2022-07-26 09:50:57", "commits": 9 } ], "_score": 5.184691430817599, "_indexed": true, "_nocasepkg": "mkomics", "_universes": [ "stamats" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.8", "date": "2026-07-06T06:48:10.000Z", "distro": "resolute", "commit": "799e9de1f4830d06f584674ddb1b3287e7c2b02a", "fileid": "https://r2.ropensci.org/d8dadbbe5348ef0517a89489135883189719ab1c6201a1219912eb75d4ff372b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stamats/actions/runs/28772990297" }, { "r": "4.6.1", "os": "linux", "version": "0.8", "date": "2026-07-06T06:48:56.000Z", "distro": "resolute", "commit": "799e9de1f4830d06f584674ddb1b3287e7c2b02a", "fileid": "https://r2.ropensci.org/0e092b056db00070b9fc3fc746e84416b5cdfe9df5a96c8fa5ef33e9ea989606", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stamats/actions/runs/28772990297" }, { "r": "4.5.3", "os": "mac", "version": "0.8", "date": "2026-07-06T06:48:53.000Z", "commit": "799e9de1f4830d06f584674ddb1b3287e7c2b02a", "fileid": "https://r2.ropensci.org/a9a28784962f923dd7051e01b096988b423e2ba53f9462ca1894b0f39824a8e4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stamats/actions/runs/28772990297" }, { "r": "4.6.1", "os": "mac", "version": "0.8", "date": "2026-07-06T06:48:24.000Z", "commit": "799e9de1f4830d06f584674ddb1b3287e7c2b02a", "fileid": "https://r2.ropensci.org/67f1c9aae260dc19ea0814424d53d6af9cb41fa4967b94a9a4ffbb2a770f5073", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stamats/actions/runs/28772990297" }, { "r": "4.6.0", "os": "wasm", "version": "0.8", "date": "2026-07-06T06:48:13.000Z", "commit": "799e9de1f4830d06f584674ddb1b3287e7c2b02a", "fileid": "https://r2.ropensci.org/0159d01f1b0dddd415417ce9b6383fd3f6eb9d125d9215868202a03903ae8991", "status": "success", "buildurl": "https://github.com/r-universe/stamats/actions/runs/28772990297" }, { "r": "4.7.0", "os": "win", "version": "0.8", "date": "2026-07-06T06:47:13.000Z", "commit": "799e9de1f4830d06f584674ddb1b3287e7c2b02a", "fileid": "https://r2.ropensci.org/cd0ae34eb1acd0ff5b599e3af8e168983c7d5568cb32727080e8e69f47f670b8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stamats/actions/runs/28772990297" }, { "r": "4.5.3", "os": "win", "version": "0.8", "date": "2026-07-06T06:47:17.000Z", "commit": "799e9de1f4830d06f584674ddb1b3287e7c2b02a", "fileid": "https://r2.ropensci.org/2a98a2a4a8551dff605c60b207f4847535f2494827c25230c91a6881c55f6983", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stamats/actions/runs/28772990297" }, { "r": "4.6.1", "os": "win", "version": "0.8", "date": "2026-07-06T06:47:28.000Z", "commit": "799e9de1f4830d06f584674ddb1b3287e7c2b02a", "fileid": "https://r2.ropensci.org/f95e8991a86a5851b4a6350c0a6e98390da094311330bd0088e3c37bd72b86c7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/stamats/actions/runs/28772990297" } ] }