{ "_id": "6a23d762530b9bc726be55bb", "Package": "mineCitrus", "Type": "Package", "Title": "Extract and Analyze Median Molecule Intensity from 'citrus'\nOutput", "Version": "1.0.0", "Date": "2018-07-05", "Author": "Allison Throm", "Maintainer": "Allison Throm ", "Description": "Citrus is a computational technique developed for the\nanalysis of high dimensional cytometry data sets. This package\nextracts, statistically analyzes, and visualizes marker\nexpression from 'citrus' data. This code was used to generate\ndata for Figures 3 and 4 in the forthcoming manuscript: Throm\net al. “Identification of Enhanced Interferon-Gamma Signaling\nin Polyarticular Juvenile Idiopathic Arthritis with Mass\nCytometry”, JCI-Insight. For more information on Citrus, please\nsee: Bruggner et al. (2014) . To\ndownload the 'citrus' package, please see\n.", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "6.0.1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-06 08:14:13 UTC", "User": "root" }, "Repository": "https://cran.r-universe.dev", "Date/Publication": "2018-07-05 12:40:03 UTC", "RemoteUrl": "https://github.com/cran/mineCitrus", "RemoteRef": "HEAD", "RemoteSha": "e1dfedf4abab2cdacce65ee63b86f109cac0e19d", "MD5sum": "532b265851b54c62a8de3e1d99f11ad2", "_user": "cran", "_type": "src", "_file": "mineCitrus_1.0.0.tar.gz", "_fileid": "7227f938e499a2a3ba05b21c36a3eaacbf468d99e27cb13dd459f978d5a1cef3", "_filesize": 1635138, "_sha256": "7227f938e499a2a3ba05b21c36a3eaacbf468d99e27cb13dd459f978d5a1cef3", "_created": "2026-06-06T08:14:13.000Z", "_published": "2026-06-06T08:16:34.592Z", "_distro": "noble", "_jobs": [ { "job": 79863553579, "time": 105, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7452762976" }, { "job": 79863553582, "time": 107, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7452763201" }, { "job": 79863410041, "time": 163, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7452751443" }, { "job": 79863553584, "time": 98, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7452762294" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/27057028826", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/mineCitrus", "_commit": { "id": "e1dfedf4abab2cdacce65ee63b86f109cac0e19d", "author": "Allison Throm ", "committer": "cran-robot ", "message": "version 1.0.0\n", "time": 1530794403 }, "_maintainer": { "name": "Allison Throm", "email": "throm@wustl.edu" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 1, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 143, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/mineCitrus" }, "_searchresults": 40, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/mineCitrus.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2018-07-05" } ], "_exports": [ "allmeds", "classclustermeds", "clustermeds", "difMarkerPlots", "difMarkerPlots2", "filterMarker", "findclust", "findSig", "plotdif", "plotdif2", "posthoc", "processforanova", "sortmat" ], "_datasets": [ { "name": "citrus.combinedFCSSet", "title": "Cytometry data set for example of Citrus data set from nolanlab/citrus", "object": "citrus.combinedFCSSet", "class": [ "citrus.combinedFCSSet" ], "fields": [], "table": false, "tojson": false }, { "name": "citrus.foldClustering", "title": "Clustering data for example of Citrus data set from nolanlab/citrus", "object": "citrus.foldClustering", "class": [ "citrus.foldClustering" ], "fields": [], "table": false, "tojson": false }, { "name": "citrus.foldFeatureSet", "title": "Correlation data for example of Citrus data set from nolanlab/citrus", "object": "citrus.foldFeatureSet", "class": [ "citrus.foldFeatureSet" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "allmeds", "title": "Gets matrices of medians for each individual sample for all measured parameters for all clusters", "topics": [ "allmeds" ] }, { "page": "citrus.combinedFCSSet", "title": "Cytometry data set for example of Citrus data set from nolanlab/citrus", "topics": [ "citrus.combinedFCSSet" ] }, { "page": "citrus.foldClustering", "title": "Clustering data for example of Citrus data set from nolanlab/citrus", "topics": [ "citrus.foldClustering" ] }, { "page": "citrus.foldFeatureSet", "title": "Correlation data for example of Citrus data set from nolanlab/citrus", "topics": [ "citrus.foldFeatureSet" ] }, { "page": "classclustermeds", "title": "Gets matrices of medians for each individual sample for all measured parameters for all clusters", "topics": [ "classclustermeds" ] }, { "page": "clustermeds", "title": "Gets matrix of medians for desired measured features for all clusters meeting threshold requirements specified in Citrus", "topics": [ "clustermeds" ] }, { "page": "difMarkerPlots", "title": "Plot dot plots of features where both clusters are significantly different from the reference cluster without processing data before hand", "topics": [ "difMarkerPlots" ] }, { "page": "difMarkerPlots2", "title": "Plot dot plots of features where one cluster is significantly different from the reference cluster without processing data before hand", "topics": [ "difMarkerPlots2" ] }, { "page": "filterMarker", "title": "Filters list of data matrices with columns corresponding to the measured parameters of interest", "topics": [ "filterMarker" ] }, { "page": "findclust", "title": "Filters list to contain only desired clusters", "topics": [ "findclust" ] }, { "page": "findSig", "title": "Assesses significance of ANOVA and t-test results", "topics": [ "findSig" ] }, { "page": "plotdif", "title": "Plot dot plots of features where both clusters are significantly different from the reference cluster", "topics": [ "plotdif" ] }, { "page": "plotdif2", "title": "Plot dot plots of features where one cluster is significantly different from the reference cluster", "topics": [ "plotdif2" ] }, { "page": "posthoc", "title": "Runs ANOVA and t-tests comparing clusters and markers in clusters", "topics": [ "posthoc" ] }, { "page": "processforanova", "title": "Processes cluster signaling data in form for statistical analysis", "topics": [ "processforanova" ] }, { "page": "sortmat", "title": "Reorders to rows (corresponding to different clusters) of a matrix of medians to a desired order", "topics": [ "sortmat" ] } ], "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gtable", "isoband", "labeling", "lifecycle", "R6", "RColorBrewer", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_score": 1.6020599913279625, "_indexed": true, "_nocasepkg": "minecitrus", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-06-06T08:15:51.000Z", "distro": "noble", "commit": "e1dfedf4abab2cdacce65ee63b86f109cac0e19d", "fileid": "275b3b451185b1bd5d1b4896709bdb64802010518459b6765d59019fcf72292a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27057028826" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-06-06T08:15:53.000Z", "distro": "noble", "commit": "e1dfedf4abab2cdacce65ee63b86f109cac0e19d", "fileid": "c9d1cc92ad6d182fc8220474f6bce5b7db9792b5fcc737b5d22532aaf4d6e9fd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27057028826" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-06-06T08:16:07.000Z", "commit": "e1dfedf4abab2cdacce65ee63b86f109cac0e19d", "fileid": "f5aa89c8907fa13be36ef6c489f08e84eb329a4f02f82229f56a65225b5d2dcd", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/27057028826" } ] }