{ "_id": "6a1acdfe1d7bb097a09df73b", "Package": "flowStats", "Type": "Package", "Title": "Statistical methods for the analysis of flow cytometry data", "Version": "4.25.0", "Author": "Florian Hahne, Nishant Gopalakrishnan, Alireza Hadj\nKhodabakhshi, Chao-Jen Wong, Kyongryun Lee", "Maintainer": "Greg Finak , Mike Jiang ", "Description": "Methods and functionality to analyse flow data that is\nbeyond the basic infrastructure provided by the flowCore\npackage.", "Encoding": "UTF-8", "License": "Artistic-2.0", "Lazyload": "yes", "URL": "http://www.github.com/RGLab/flowStats", "BugReports": "http://www.github.com/RGLab/flowStats/issues", "biocViews": "ImmunoOncology, FlowCytometry, CellBasedAssays", "RoxygenNote": "7.3.0", "Config/pak/sysreqs": "make libjpeg-dev libpng-dev libxml2-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:33:51 UTC", "RemoteUrl": "https://github.com/bioc/flowStats", "RemoteRef": "HEAD", "RemoteSha": "78c4b7cdd273fa1db3119f613c1686b118133fb3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:11:30 UTC", "User": "root" }, "MD5sum": "a60e770c046395060f5604cc31a08908", "_user": "bioc", "_type": "src", "_file": "flowStats_4.25.0.tar.gz", "_fileid": "48ac190a4335dd62ad25dfc81bed00f2fff641cc9e4ef72fdf8b0e1088258037", "_filesize": 11794589, "_sha256": "48ac190a4335dd62ad25dfc81bed00f2fff641cc9e4ef72fdf8b0e1088258037", "_created": "2026-05-30T08:11:30.000Z", "_published": "2026-05-30T11:46:06.501Z", "_jobs": [ { "job": 78635760292, "time": 188, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306751852" }, { "job": 78635760302, "time": 347, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7306766882" }, { "job": 78635760301, "time": 328, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306765069" }, { "job": 78635760293, "time": 177, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7307939315" }, { "job": 78635760289, "time": 179, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7307939787" }, { "job": 78635511922, "time": 294, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306733690" }, { "job": 78635760297, "time": 164, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306749434" }, { "job": 78635760294, "time": 224, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7306755166" }, { "job": 78635760296, "time": 223, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7306755065" }, { "job": 78635760298, "time": 259, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7306758559" } ], "_bioccheck": { "error": 2, "warning": 7, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678831604", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/flowStats", "_commit": { "id": "78c4b7cdd273fa1db3119f613c1686b118133fb3", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379631 }, "_maintainer": { "name": "Greg Finak", "email": "mike@ozette.com", "login": "gfinak", "twitter": "@GregFinak", "description": "", "uuid": 1385593 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.2", "role": "Depends" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "flowCore", "version": ">= 1.99.6", "role": "Imports" }, { "package": "flowWorkspace", "role": "Imports" }, { "package": "ncdfFlow", "version": ">= 2.19.5", "role": "Imports" }, { "package": "flowViz", "role": "Imports" }, { "package": "fda", "version": ">= 2.2.6", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "KernSmooth", "role": "Imports" }, { "package": "lattice", "role": "Imports" }, { "package": "ks", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "rrcov", "role": "Imports" }, { "package": "corpcor", "role": "Imports" }, { "package": "mnormt", "role": "Imports" }, { "package": "clue", "role": "Imports" }, { "package": "xtable", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "openCyto", "role": "Suggests" }, { "package": "ggcyto", "role": "Suggests" }, { "package": "ggridges", "role": "Suggests" }, { "package": "RBGL", "role": "Enhances" }, { "package": "graph", "role": "Enhances" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "4.25.0", "bioc": "3.24" }, { "branch": "release", "version": "4.24.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "flowcytometry", "cellbasedassays" ], "_stars": 14, "_contributors": [ { "user": "jacobpwagner", "count": 75, "uuid": 43548373 }, { "user": "gfinak", "count": 36, "uuid": 1385593 }, { "user": "dtenenba", "count": 27, "uuid": 2286826 }, { "user": "nturaga", "count": 26, "uuid": 2746443 }, { "user": "ramhiser", "count": 8, "uuid": 261183 }, { "user": "mikejiang", "count": 7, "uuid": 1385649 }, { "user": "hpages", "count": 4, "uuid": 8810451 }, { "user": "vobencha", "count": 4, "uuid": 2466173 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 }, { "user": "kayla-morrell", "count": 2, "uuid": 32339524 }, { "user": "kevinushey", "count": 1, "uuid": 1976582 }, { "user": "sonali-bioc", "count": 1, "uuid": 6373953 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 1278, "source": "https://www.bioconductor.org/packages/stats/bioc/flowStats" }, "_mentions": 19, "_devurl": "https://github.com/rglab/flowstats", "_searchresults": 209, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/flowStats.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_homeurl": "https://github.com/rglab/flowstats", "_realowner": "bioc", "_cranurl": false, "_exports": [ "%in%", "binByRef", "calcPBChiSquare", "calcPearsonChi", "curv1Filter", "curv2Filter", "curvPeaks", "flowClust2Prior", "gate_singlet", "gaussNorm", "gpaSet", "iProcrustes", "lymphGate", "mkPrior", "norm2Filter", "normalize", "normQA", "oneDGate", "overton_like", "plotBins", "plotPrior", "proBin", "quadrantGate", "rangeFilter", "rangeGate", "SimulateMixture", "singletGate", "spillover", "spillover_match", "spillover_ng", "warpSet" ], "_datasets": [ { "name": "BackGating", "title": "Sample backgating results", "object": "BackGating", "file": "BackGating.rda", "class": [ "data.frame" ], "fields": [ "FSC", "SSC", "population", "type", "sample", "peak", "channel" ], "rows": 12762, "table": true, "tojson": true }, { "name": "ITN", "title": "Sample flow cytometry data", "object": "ITN", "file": "ITN.rda", "class": [ "flowSet" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "flowStats-package", "title": "Statistical methods for flow cytometry data analysis", "topics": [ "flowStats-package", "flowStats" ] }, { "page": "addName-methods", "title": "These methods are copied from flowViz to eliminate its dependency on curv1Filter and curv2Filter", "topics": [ "addName,curv1Filter,character-method", "addName,curv1Filter,logical-method", "addName,curv2Filter,character-method", "addName,curv2Filter,logical-method" ] }, { "page": "autoGate", "title": "Automated gating of single populations in 2D", "topics": [ "autoGate" ] }, { "page": "BackGating", "title": "Sample backgating results", "topics": [ "BackGating" ] }, { "page": "binByRef", "title": "Bin a test data set using bins previously created by probability binning a control dataset", "topics": [ "binByRef" ] }, { "page": "calcPBChiSquare", "title": "Probability binning metirc for comparing the probability binned datasets", "topics": [ "calcPBChiSquare" ] }, { "page": "calcPearsonChi", "title": "Pearsons chi-square statistic for comparing the probability binned datasets", "topics": [ "calcPearsonChi" ] }, { "page": "curv1Filter-class", "title": "Class \"curv1Filter\"", "topics": [ "%in%,flowFrame,curv1Filter-method", "curv1Filter", "curv1Filter-class", "show,curv1Filter-method", "summarizeFilter,multipleFilterResult,curv1Filter-method" ] }, { "page": "curv2Filter-class", "title": "Class \"curv2Filter\"", "topics": [ "%in%,flowFrame,curv2Filter-method", "curv2Filter", "curv2Filter-class", "show,curv2Filter-method", "summarizeFilter,multipleFilterResult,curv2Filter-method" ] }, { "page": "curvPeaks", "title": "Parse curv1Filter output", "topics": [ "curvPeaks" ] }, { "page": "density1d", "title": "Find most likely separation between positive and negative populations in 1D", "topics": [ "density1d" ] }, { "page": "ellipse", "title": "convert ellipse from cov/mu to points used to plot priors", "topics": [ "ellipse" ] }, { "page": "fdPar", "title": "The version of fdPar from fda 2.4.0 because the new API changes the output. (specifically res$fd$coefs) and thus breaks the landmarkreg call.", "topics": [ "fdPar" ] }, { "page": "flowClust2Prior", "title": "Generate a prior specification based on a flowClust model This function generates a prior specification based on a flowClust fit object It can be passed to a second round of flowClust() with usePrior=\"yes\" The prior could be estimated from a single sample, for example, and then used to speed up the convergence for other samples.", "topics": [ "flowClust2Prior" ] }, { "page": "gate_singlet", "title": "Creates a singlet polygon gate using the prediction bands from a robust linear model", "topics": [ "gate_singlet", "singletGate" ] }, { "page": "gaussNorm", "title": "Per-channel normalization based on landmark registration", "topics": [ "gaussNorm" ] }, { "page": "gpaSet", "title": "Multi-dimensional normalization of flow cytometry data", "topics": [ "gpaSet" ] }, { "page": "idFeaturesByBackgating", "title": "(Internal use only) Identify features of flow cytometry data using backgating", "topics": [ "idFeatures", "idFeaturesByBackgating" ] }, { "page": "iProcrustes", "title": "Procrustes analysis. Using singular value decomposition (SVD) to determine a linear transformation to align the points in X to the points in a reference matrix Y.", "topics": [ "iProcrustes" ] }, { "page": "ITN", "title": "Sample flow cytometry data", "topics": [ "ITN" ] }, { "page": "landmarkMatrix", "title": "Compute and cluster high density regions in 1D", "topics": [ "landmarkMatrix" ] }, { "page": "lymphGate", "title": "Automated gating of elliptical cell populations in 2D.", "topics": [ "%in%,flowFrame,lymphFilter-method", "lymphFilter", "lymphFilter-class", "lymphGate" ] }, { "page": "mkPrior", "title": "Generate a flowClust prior specification", "topics": [ "mkPrior", "mkPrior,list,flowSet,ANY,missing-method", "mkPrior,list,flowSet,missing,missing-method", "mkPrior,missing,flowFrame,missing,missing-method", "mkPrior,missing,flowSet,ANY,missing-method", "mkPrior,polygonGate,flowFrame,missing,missing-method", "mkPrior,polygonGate,flowFrame,numeric,matrix-method", "mkPrior,rectangleGate,flowFrame,missing,missing-method", "mkPrior,rectangleGate,flowFrame,numeric,matrix-method" ] }, { "page": "norm2Filter-class", "title": "Class \"norm2Filter\"", "topics": [ "%in%,flowFrame,norm2Filter-method", "norm2Filter", "norm2Filter-class", "show,norm2Filter-method" ] }, { "page": "normalize", "title": "normalize a GatingSet imported with flowWorkspace, using sequential normalization on the manual gates in the GatingHierarchy.", "topics": [ "normalize", "normalize,GatingSet,missing-method", "normalize,GatingSetInternal,missing-method", "normalize-methods" ] }, { "page": "normQA", "title": "Normalization quality assessment", "topics": [ "normQA" ] }, { "page": "overton_like", "title": "Overton-like subtraction of densities.", "topics": [ "overton_like" ] }, { "page": "plotBins", "title": "Plots the probability bins overlaid with flowFrame data", "topics": [ "plotBins" ] }, { "page": "plotPrior", "title": "Plots a flowClust prior over some data.", "topics": [ "plotPrior" ] }, { "page": "proBin", "title": "Probability binning - a metric for evaluating multivariate differences", "topics": [ "proBin" ] }, { "page": "quadrantGate", "title": "Automated quad gating", "topics": [ "quadrantGate" ] }, { "page": "rangeGate", "title": "Find most likely separation between positive and negative populations in 1D", "topics": [ "%in%,flowFrame,rangeFilter-method", "oneDGate", "rangeFilter", "rangeFilter-class", "rangeGate" ] }, { "page": "SimulateMixture", "title": "Random Generation from a t Mixture Model with Box-Cox Transformation", "topics": [ "SimulateMixture" ] }, { "page": "spillover_match-flowSet", "title": "Construct a 'flowSet' for use with 'spillover' by matching channel names to compensation control filenames", "topics": [ "spillover_match", "spillover_match,flowSet-method", "spillover_match,missing-method", "spillover_match-flowSet" ] }, { "page": "spillover_ng-flowSet", "title": "Compute a spillover matrix from a 'flowSet', simplified API", "topics": [ "spillover_ng", "spillover_ng,flowSet-method", "spillover_ng,missing-method", "spillover_ng-flowSet" ] }, { "page": "spillover-flowSet", "title": "Compute a spillover matrix from a flowSet", "topics": [ "spillover", "spillover,flowSet-method", "spillover-flowSet" ] }, { "page": "warpSet", "title": "Normalization based on landmark registration", "topics": [ "warpSet", "warpSet.cytoset", "warpSetGS", "warpSetNCDF", "warpSetNCDFLowMem" ] } ], "_rundeps": [ "abind", "ash", "BH", "Biobase", "BiocGenerics", "biocmake", "bitops", "cli", "clue", "cluster", "colorspace", "corpcor", "cpp11", "cytolib", "data.table", "DelayedArray", "deldir", "DEoptimR", "deSolve", "dir.expiry", "dplyr", "farver", "fda", "fds", "filelock", "flowCore", "flowViz", "flowWorkspace", "FNN", "generics", "ggplot2", "glue", "graph", "gtable", "hdrcde", "hexbin", "IDPmisc", "interp", "IRanges", "isoband", "jpeg", "kernlab", "KernSmooth", "ks", "labeling", "lattice", "latticeExtra", "lifecycle", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mclust", "mgcv", "mnormt", "multicool", "mvtnorm", "ncdfFlow", "nlme", "pcaPP", "pillar", "pkgconfig", "png", "pracma", "R6", "rainbow", "RBGL", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "Rgraphviz", "Rhdf5lib", "rlang", "robustbase", "RProtoBufLib", "rrcov", "S4Arrays", "S4Vectors", "S7", "scales", "SparseArray", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XML", "XVector" ], "_vignettes": [ { "source": "GettingStartedWithFlowStats.Rnw", "filename": "GettingStartedWithFlowStats.pdf", "title": "flowStats Overview", "engine": "utils::Sweave", "headings": [], "created": "2013-12-24 00:13:06", "modified": "2019-11-26 22:43:27", "commits": 7 } ], "_score": 8.392349111153543, "_indexed": true, "_nocasepkg": "flowstats", "_universes": [ "bioc", "gfinak", "rglab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "4.25.0", "date": "2026-05-30T08:15:39.000Z", "distro": "noble", "commit": "78c4b7cdd273fa1db3119f613c1686b118133fb3", "fileid": "1ef2427370a82d8f5b3e4d5a179521a14a0af7fc6c02980ec9de58ddba837bfb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678831604" }, { "r": "4.6.0", "os": "linux", "version": "4.25.0", "date": "2026-05-30T08:15:30.000Z", "distro": "noble", "commit": "78c4b7cdd273fa1db3119f613c1686b118133fb3", "fileid": "52036c67f1fbe07dbb33e5323a4e2a15a43386f85d0626d4d82cda3fad95659e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678831604" }, { "r": "4.5.3", "os": "mac", "version": "4.25.0", "date": "2026-05-30T11:44:09.000Z", "commit": "78c4b7cdd273fa1db3119f613c1686b118133fb3", "fileid": "a541d0ebe16362700043a330cf53abe3172975eadddf1962614c7d30542e7433", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678831604" }, { "r": "4.6.0", "os": "mac", "version": "4.25.0", "date": "2026-05-30T11:44:11.000Z", "commit": "78c4b7cdd273fa1db3119f613c1686b118133fb3", "fileid": "e5f21ca3e0c235550665fbd6c09e6764974208d302798764e72bf8142f8175bc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678831604" }, { "r": "4.6.0", "os": "wasm", "version": "4.25.0", "date": "2026-05-30T08:14:51.000Z", "commit": "78c4b7cdd273fa1db3119f613c1686b118133fb3", "fileid": "d6f6647b17133eb70d47982048e0656e8a5ee1d061feaca8bdb4f49e3418eb6a", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678831604" }, { "r": "4.7.0", "os": "win", "version": "4.25.0", "date": "2026-05-30T08:13:40.000Z", "commit": "78c4b7cdd273fa1db3119f613c1686b118133fb3", "fileid": "dc0c58de80d2265bfb802b6a9c08327f01f10351580675ed71802d1fdd2d2638", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678831604" }, { "r": "4.5.3", "os": "win", "version": "4.25.0", "date": "2026-05-30T08:13:31.000Z", "commit": "78c4b7cdd273fa1db3119f613c1686b118133fb3", "fileid": "63222638840a1a8bdf08cb955057cda26e22a0a57313d57fb0637b2119ca25ce", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678831604" }, { "r": "4.6.0", "os": "win", "version": "4.25.0", "date": "2026-05-30T08:13:53.000Z", "commit": "78c4b7cdd273fa1db3119f613c1686b118133fb3", "fileid": "b7a3e8f12135c72b4e7eb043300cb5e30f7d6d1e87e9ab799c09635dd71c9450", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678831604" } ] }