{ "_id": "6a1d28561d7bb097a0a3845a", "Package": "COMPASS", "Type": "Package", "Title": "Combinatorial Polyfunctionality Analysis of Single Cells", "Version": "1.51.0", "Date": "2014-07-11", "Author": "Lynn Lin, Kevin Ushey, Greg Finak, Ravio Kolde (pheatmap)", "Authors@R": "c( person(\"Lynn\", \"Lin\", role=\"aut\", email=\"llin@fhcrc.org\"),\nperson(\"Kevin\", \"Ushey\", role=\"aut\", email=\"kushey@fhcrc.org\"),\nperson(\"Greg\", \"Finak\", role=c(\"aut\",\"cre\"), email=\"gfinak@fhcrc.org\"),\nperson(\"Raivo\", \"Kolde\", role=\"ctb\", email=\"rkolde@gmail.com\",\ncomment=\"Author of 'pheatmap', which was modified and now used internally\nin COMPASS\") )", "Description": "COMPASS is a statistical framework that enables unbiased\nanalysis of antigen-specific T-cell subsets. COMPASS uses a\nBayesian hierarchical framework to model all observed\ncell-subsets and select the most likely to be antigen-specific\nwhile regularizing the small cell counts that often arise in\nmulti-parameter space. The model provides a posterior\nprobability of specificity for each cell subset and each\nsample, which can be used to profile a subject's immune\nresponse to external stimuli such as infection or vaccination.", "License": "Artistic-2.0", "BugReports": "https://github.com/RGLab/COMPASS/issues", "VignetteBuilder": "knitr", "Maintainer": "Greg Finak ", "LazyLoad": "yes", "LazyData": "yes", "biocViews": "ImmunoOncology, FlowCytometry", "Encoding": "UTF-8", "RoxygenNote": "7.1.1", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:38:38 UTC", "RemoteUrl": "https://github.com/bioc/COMPASS", "RemoteRef": "HEAD", "RemoteSha": "ebde741d93aad3647f53f494f22181473eec3f72", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 09:13:46 UTC", "User": "root" }, "MD5sum": "d0b0381454581d7ec5e6f677a3b2e3a5", "_user": "bioc", "_type": "src", "_file": "COMPASS_1.51.0.tar.gz", "_fileid": "3de75d249c1c323a135dc1a5f73cdc7313d4439c5ec6dcb9d77205a7181c097e", "_filesize": 1310443, "_sha256": "3de75d249c1c323a135dc1a5f73cdc7313d4439c5ec6dcb9d77205a7181c097e", "_created": "2026-05-30T09:13:46.000Z", "_published": "2026-06-01T06:36:06.775Z", "_distro": "noble", "_jobs": [ { "job": 78798360587, "time": 185, "config": "bioc-checks", "r": "4.6.0", "check": "FAILURE", "artifact": "" }, { "job": 78798360661, "time": 206, "config": "linux-devel-arm64", "r": "4.7.0", "check": "FAIL", "artifact": "" }, { "job": 78798360691, "time": 216, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "FAIL", "artifact": "" }, { "job": 78798360683, "time": 169, "config": "linux-release-arm64", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 78798360652, "time": 202, "config": "linux-release-x86_64", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 78798361054, "time": 150, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308293531" }, { "job": 78798360751, "time": 312, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "ERROR", "artifact": "7324839255" }, { "job": 78798360737, "time": 72, "config": "macos-release-arm64", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 78798360780, "time": 207, "config": "macos-release-x86_64", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 78798360709, "time": 354, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307097174" }, { "job": 78798360591, "time": 291, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 78798360711, "time": 107, "config": "windows-devel", "r": "4.7.0", "check": "FAIL", "artifact": "" }, { "job": 78798361288, "time": 198, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307145320" }, { "job": 78798360721, "time": 121, "config": "windows-release", "r": "4.6.0", "check": "FAIL", "artifact": "" } ], "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26658037109", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/COMPASS", "_commit": { "id": "ebde741d93aad3647f53f494f22181473eec3f72", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379918 }, "_maintainer": { "name": "Greg Finak", "email": "gfinak@fhcrc.org" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.3", "role": "Depends" }, { "package": "Rcpp", "version": ">= 0.11.0", "role": "LinkingTo" }, { "package": "methods", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "knitr", "role": "Imports" }, { "package": "abind", "role": "Imports" }, { "package": "clue", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "pdist", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "BiocStyle", "role": "Imports" }, { "package": "rmarkdown", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "coda", "role": "Imports" }, { "package": "flowWorkspace", "version": ">= 3.33.1", "role": "Suggests" }, { "package": "flowCore", "role": "Suggests" }, { "package": "ncdfFlow", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "flowWorkspaceData", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "progress", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.51.0", "bioc": "3.24" }, { "branch": "release", "version": "1.49.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "flowcytometry", "cpp" ], "_stars": 8, "_contributors": [ { "user": "kevinushey", "count": 207, "uuid": 1976582 }, { "user": "gfinak", "count": 179, "uuid": 1385593 }, { "user": "dtenenba", "count": 12, "uuid": 2286826 }, { "user": "nturaga", "count": 10, "uuid": 2746443 }, { "user": "llynn", "count": 6, "uuid": 3037736 }, { "user": "vobencha", "count": 4, "uuid": 2466173 }, { "user": "malisas", "count": 3, "uuid": 16787492 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "link-ny", "count": 2, "uuid": 4392950 }, { "user": "erictleung", "count": 1, "uuid": 2754821 }, { "user": "kayla-morrell", "count": 1, "uuid": 32339524 }, { "user": "ptvan", "count": 1, "uuid": 8515847 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 486, "source": "https://www.bioconductor.org/packages/stats/bioc/COMPASS" }, "_mentions": 614, "_devurl": "https://github.com/rglab/compass", "_searchresults": 51, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/COMPASS.html", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/rglab/compass", "_realowner": "bioc", "_cranurl": false, "_exports": [ "categories", "CellCounts", "Combinations", "COMPASS", "COMPASSContainer", "COMPASSContainerFromGatingSet", "COMPASSDescription", "COMPASSDescription<-", "COMPASSfitToCountsTable", "COMPASSMCMCDiagnosis", "FunctionalityScore", "getCounts", "GetThresholdedIntensities", "markers", "metadata", "metadata<-", "pheatmap", "plot2", "plotCOMPASSResultStack", "PolyfunctionalityScore", "Posterior", "PosteriorDiff", "PosteriorLogDiff", "PosteriorPs", "PosteriorPu", "Response", "scores", "select_compass_pops", "shinyCOMPASS", "shinyCOMPASSDeps", "SimpleCOMPASS", "TotalCellCounts", "translate_marker_names", "transpose_list", "UniqueCombinations" ], "_datasets": [ { "name": "CC", "title": "Simulated COMPASSContainer", "object": "COMPASS", "class": [ "COMPASSContainer" ], "fields": [], "table": false, "tojson": false }, { "name": "CR", "title": "Simulated COMPASS fit", "object": "COMPASS", "class": [ "COMPASSResult" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "COMPASS-package", "title": "COMPASS (Combinatorial Polyfunctionality Analysis of Single-Cells)", "topics": [ "COMPASS-package" ] }, { "page": "categories", "title": "Categories", "topics": [ "categories" ] }, { "page": "CellCounts", "title": "Compute Number of Cells Positive for Certain Cytokine Combinations", "topics": [ "CellCounts" ] }, { "page": "Combinations", "title": "Generate Combinations", "topics": [ "Combinations" ] }, { "page": "COMPASS", "title": "Fit the COMPASS Model", "topics": [ "COMPASS" ] }, { "page": "COMPASSContainer", "title": "Generate the Data Object used by COMPASS", "topics": [ "COMPASSContainer" ] }, { "page": "COMPASSContainer-data", "title": "Simulated COMPASSContainer", "topics": [ "CC", "COMPASSContainer-data" ] }, { "page": "COMPASSContainerFromGatingSet", "title": "Create a COMPASS Container from a GatingSet", "topics": [ "COMPASSContainerFromGatingSet" ] }, { "page": "COMPASSDescription", "title": "Get and Set the Description for the Shiny Application", "topics": [ "COMPASSDescription", "COMPASSDescription<-" ] }, { "page": "COMPASSfitToCountsTable", "title": "Extract a table of counts from a COMPASSResult object", "topics": [ "COMPASSfitToCountsTable" ] }, { "page": "COMPASSMCMCDiagnosis", "title": "Diagnostic of a set of COMPASS Models.", "topics": [ "COMPASSMCMCDiagnosis" ] }, { "page": "COMPASSResult-accessors", "title": "COMPASSResult Accessors", "topics": [ "COMPASSResult-accessors", "Gamma", "MeanGamma" ] }, { "page": "COMPASSResult-data", "title": "Simulated COMPASS fit", "topics": [ "COMPASSResult-data", "CR" ] }, { "page": "FunctionalityScore", "title": "Compute the Functionality Score for each subject fit in a COMPASS model", "topics": [ "FunctionalityScore", "FunctionalityScore.COMPASSResult", "FunctionalityScore.default" ] }, { "page": "getCounts", "title": "Get a data.table of counts of polyfunctional subsets", "topics": [ "getCounts" ] }, { "page": "GetThresholdedIntensities", "title": "Extract Thresholded Intensities from a GatingSet", "topics": [ "GetThresholdedIntensities" ] }, { "page": "markers", "title": "Markers", "topics": [ "markers" ] }, { "page": "melt_", "title": "Make a 'Wide' data set 'Long'", "topics": [ "melt_", "melt_.data.frame", "melt_.matrix" ] }, { "page": "merge.COMPASSContainer", "title": "Merge Two COMPASSContainers", "topics": [ "merge.COMPASSContainer" ] }, { "page": "metadata", "title": "Metadata", "topics": [ "metadata", "metadata.COMPASSContainer", "metadata.COMPASSResult", "metadata<-", "metadata<-.COMPASSContainer" ] }, { "page": "pheatmap", "title": "A function to draw clustered heatmaps.", "topics": [ "pheatmap" ] }, { "page": "plot.COMPASSResult", "title": "Plot a COMPASSResult", "topics": [ "plot", "plot.COMPASSResult" ] }, { "page": "plot2", "title": "Plot a pair of COMPASSResults", "topics": [ "plot2" ] }, { "page": "plotCOMPASSResultStack", "title": "Plot multiple COMPASSResults", "topics": [ "plotCOMPASSResultStack" ] }, { "page": "PolyfunctionalityScore", "title": "Compute the Polyfunctionality Score for each subject fit in a COMPASS model", "topics": [ "PolyfunctionalityScore", "PolyfunctionalityScore.COMPASSResult", "PolyfunctionalityScore.default" ] }, { "page": "Posterior", "title": "Retrieve Posterior Measures from a COMPASS fit", "topics": [ "Posterior", "PosteriorDiff", "PosteriorLogDiff", "PosteriorPs", "PosteriorPu" ] }, { "page": "print.COMPASSContainer", "title": "Print a COMPASSContainer Object", "topics": [ "print.COMPASSContainer" ] }, { "page": "print.COMPASSResult", "title": "Print a COMPASSResult Object", "topics": [ "print.COMPASSResult" ] }, { "page": "Response", "title": "Compute a response probability from COMPASS mcmc samples.", "topics": [ "Response", "Response.COMPASSResult" ] }, { "page": "scores", "title": "Fetch the table of scores and metadata from a COMPASSResult Object", "topics": [ "scores" ] }, { "page": "select_compass_pops", "title": "Flag COMPASS boolean populations", "topics": [ "select_compass_pops" ] }, { "page": "shinyCOMPASS", "title": "Start a Shiny Application for Visualizing COMPASS Results", "topics": [ "shinyCOMPASS" ] }, { "page": "shinyCOMPASSDeps", "title": "List Shiny Dependencies", "topics": [ "shinyCOMPASSDeps" ] }, { "page": "SimpleCOMPASS", "title": "Fit the discrete COMPASS Model", "topics": [ "SimpleCOMPASS" ] }, { "page": "subset.COMPASSContainer", "title": "Subset a COMPASSContainer", "topics": [ "subset.COMPASSContainer" ] }, { "page": "summary.COMPASSContainer", "title": "Summarize a COMPASSContainer Object", "topics": [ "summary.COMPASSContainer" ] }, { "page": "summary.COMPASSResult", "title": "Summarize a COMPASSResult Object", "topics": [ "summary.COMPASSResult" ] }, { "page": "TotalCellCounts", "title": "Compute Total Cell Counts", "topics": [ "TotalCellCounts" ] }, { "page": "translate_marker_names", "title": "Translate marker names to format use by COMPASS", "topics": [ "translate_marker_names" ] }, { "page": "transpose_list", "title": "Transpose a List", "topics": [ "transpose_list" ] }, { "page": "UniqueCombinations", "title": "Generate Unique Combinations", "topics": [ "UniqueCombinations", "UniqueCombinations.COMPASSContainer", "UniqueCombinations.default" ] } ], "_readme": "https://github.com/bioc/COMPASS/raw/HEAD/README.md", "_rundeps": [ "abind", "base64enc", "BiocManager", "BiocStyle", "bookdown", "bslib", "cachem", "cli", "clue", "cluster", "coda", "codetools", "cpp11", "data.table", "digest", "dplyr", "evaluate", "farver", "fastmap", "fontawesome", "foreach", "fs", "generics", "glue", "highr", "htmltools", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "magrittr", "memoise", "mime", "pdist", "pillar", "pkgconfig", "plyr", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "rlang", "rmarkdown", "sass", "scales", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "withr", "xfun", "yaml" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "COMPASS.Rmd", "filename": "COMPASS.html", "title": "COMPASS", "engine": "knitr::docco_linear", "headings": [ "COMPASS - Combinatorial Polyfunctionality Analysis of Single Cells", "Introduction", "Example", "data", "counts", "metadata", "Interoperation with flowWorkspace", "Citations" ], "created": "2014-04-11 21:21:21", "modified": "2015-06-14 15:59:57", "commits": 3 }, { "source": "SimpleCOMPASS.Rmd", "filename": "SimpleCOMPASS.pdf", "title": "How to use the SimpleCOMPASS Interface", "author": "Greg Finak", "engine": "knitr::rmarkdown", "headings": [ "Purpose", "Prerequisites", "Using SimpleCOMPASS", "Reading tabular ICS data", "Formatting the data", "Preparation", "Step 1. Separate the metadata and count data", "2. Split the count matrix into stimulated and non-stimulated counts.", "3. A Unique Sample Specific Identifier", "4. Name and order rows of all the matrices.", "5. Reformat cell population names.", "6. Last column should be the all-negative boolean combination.", "Fit a COMPASS model", "Visualization of results", "References" ], "created": "2018-03-06 15:43:30", "modified": "2020-05-12 18:30:40", "commits": 5 } ], "_score": 7.953082843912085, "_indexed": true, "_nocasepkg": "compass", "_universes": [ "bioc", "rglab" ], "_binaries": [ { "r": "4.6.0", "os": "linux", "version": "1.49.0", "date": "2026-04-03T09:35:40.000Z", "distro": "noble", "arch": "aarch64", "commit": "43c7ae7f954f1a996d00037d89df820fc9e6fdd2", "fileid": "af788413dcf087e51667a67bb57f6224c4046bea36daabf26de9c9b5e46f2568", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/23941472866" }, { "r": "4.6.0", "os": "mac", "version": "1.49.0", "date": "2026-04-03T09:37:51.000Z", "arch": "aarch64", "commit": "43c7ae7f954f1a996d00037d89df820fc9e6fdd2", "fileid": "8d8ed29f68a0f9be27195636fae073145bb05f2ae3593b9b8716cc3e77237de3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/23941472866" }, { "r": "4.6.0", "os": "mac", "version": "1.49.0", "date": "2026-04-03T09:40:23.000Z", "arch": "x86_64", "commit": "43c7ae7f954f1a996d00037d89df820fc9e6fdd2", "fileid": "76c6c80000020a726722b71cbf39b842d1ae1bd3d97a9d656e14d0611b773ed1", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/23941472866" }, { "r": "4.7.0", "os": "win", "version": "1.49.0", "date": "2026-04-03T09:34:48.000Z", "arch": "x86_64", "commit": "43c7ae7f954f1a996d00037d89df820fc9e6fdd2", "fileid": "e44733605ff156b08c5218333f577a13132c8209da644a609c06237e458bd513", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/23941472866" }, { "r": "4.6.0", "os": "win", "version": "1.49.0", "date": "2026-04-03T09:34:47.000Z", "arch": "x86_64", "commit": "43c7ae7f954f1a996d00037d89df820fc9e6fdd2", "fileid": "0f67ef2800c8e091ad2d1ac4e714130d0bbec5eec9a533e252c89c4fe63d7c91", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/23941472866" }, { "r": "4.6.0", "os": "linux", "version": "1.51.0", "date": "2026-04-30T16:37:28.000Z", "distro": "noble", "arch": "x86_64", "commit": "ebde741d93aad3647f53f494f22181473eec3f72", "fileid": "514ffc3b392461855f3596ab0f77c608a9e822915259d71a4d2aace9254707ea", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25175666052" }, { "r": "4.5.1", "os": "wasm", "version": "1.51.0", "date": "2026-04-30T16:55:45.000Z", "arch": "emscripten", "commit": "ebde741d93aad3647f53f494f22181473eec3f72", "fileid": "e793ed840d390141eeaefee8be568350b5482d592c31c02d94d54d8ffd4c18e5", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25175666052" }, { "r": "4.5.3", "os": "mac", "version": "1.51.0", "date": "2026-05-30T12:47:42.000Z", "arch": "aarch64", "commit": "ebde741d93aad3647f53f494f22181473eec3f72", "fileid": "bec9b7418d6461ec376e4dc04132b4f988d6ee6b0e40fbc7299c1ba2810be3e5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26658037109" }, { "r": "4.5.3", "os": "mac", "version": "1.51.0", "date": "2026-06-01T06:33:47.000Z", "arch": "x86_64", "commit": "ebde741d93aad3647f53f494f22181473eec3f72", "fileid": "a9d368fe5e938cd57218ed40dd0cbcc1e2e584624393e000b2c57d3d1c40eee7", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26658037109" }, { "r": "4.5.3", "os": "win", "version": "1.51.0", "date": "2026-05-30T09:20:47.000Z", "arch": "x86_64", "commit": "ebde741d93aad3647f53f494f22181473eec3f72", "fileid": "34173244c9e9327793f4fff900e1a16b493a1358c742827113d93ccd0f8781c1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26658037109" } ] }