{ "_id": "6a17e7f5acfb0bcc41da1cfc", "Package": "cyanoFilter", "Type": "Package", "Title": "Phytoplankton Population Identification using Cell Pigmentation\nand/or Complexity", "Version": "1.21.0", "Authors@R": "c(person(\"Oluwafemi\", \"Olusoji\", \nemail = \"oluwafemi.olusoji@uhasselt.be\",\nrole = c(\"cre\", \"aut\")),\nperson(\"Aerts\", \"Marc\", email = \"marc.aerts@uhasselt.be\", role = \"ctb\"),\nperson(\"Delaender\", \"Frederik\", email = \"frederik.delaender@unamur.be\",\nrole = \"ctb\"),\nperson(\"Neyens\", \"Thomas\", email = \"thomas.neyens@uhasselt.be\",\nrole = \"ctb\"),\nperson(\"Spaak\", \"jurg\", email = \"jurg.spaak@unamur.be\", role = \"aut\"))", "Description": "An approach to filter out and/or identify phytoplankton\ncells from all particles measured via flow cytometry pigment\nand cell complexity information. It does this using a sequence\nof one-dimensional gates on pre-defined channels measuring\ncertain pigmentation and complexity. The package is especially\ntuned for cyanobacteria, but will work fine for phytoplankton\ncommunities where there is at least one cell characteristic\nthat differentiates every phytoplankton in the community.", "URL": "https://github.com/fomotis/cyanoFilter", "BugReports": "https://github.com/fomotis/cyanoFilter/issues", "License": "MIT + file LICENSE", "biocViews": "FlowCytometry, Clustering, OneChannel", "Encoding": "UTF-8", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libjpeg-dev\nlibpng-dev libxml2-dev libssl-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:55:36 UTC", "RemoteUrl": "https://github.com/bioc/cyanoFilter", "RemoteRef": "HEAD", "RemoteSha": "68460c0fe064b9e902a9daa4ed6de0f64d34df64", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 06:32:52 UTC", "User": "root" }, "Author": "Oluwafemi Olusoji [cre, aut],\nAerts Marc [ctb],\nDelaender Frederik [ctb],\nNeyens 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"committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380936 }, "_maintainer": { "name": "Oluwafemi Olusoji", "email": "oluwafemi.olusoji@uhasselt.be", "login": "fomotisuhasselt", "description": "", "uuid": 62874198 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "Biobase", "role": "Imports" }, { "package": "flowCore", "role": "Imports" }, { "package": "flowDensity", "role": "Imports" }, { "package": "flowClust", "role": "Imports" }, { "package": "cytometree", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "GGally", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "mrfDepth", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": 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"clusterExtractp" ] }, { "page": "cyanoFilter", "title": "cyanoFilter: A package to identify and cluster phytoplankton cells contained in flow cytometry data.", "topics": [ "cyanoFilter" ] }, { "page": "DebrisFilter", "title": "the Debris class", "topics": [ "DebrisFilter" ] }, { "page": "debrisNc", "title": "gates out or assign indicators to debris particle based on their chlorophyll expression.", "topics": [ "debrisNc" ] }, { "page": "fullFlowframe", "title": "generic function for extracting the full flowframe", "topics": [ "fullFlowframe" ] }, { "page": "fullFlowframe-DebrisFilter-method", "title": "accesor method for reduced flowframe (DebrisFilter class)", "topics": [ "fullFlowframe,DebrisFilter-method" ] }, { "page": "fullFlowframe-MarginEvents-method", "title": "accesor method for the fullflowframe (MarginEvent class)", "topics": [ "fullFlowframe,MarginEvents-method" ] }, { "page": "fullFlowframe-PhytopFilter-method", "title": "accesor method for full flowframe(PhytoFilter class)", "topics": [ "fullFlowframe,PhytopFilter-method" ] }, { "page": "gateFunc", "title": "tests the accuracy of several automated gating functions on monoculture flow cytometry experiments.", "topics": [ "gateFunc" ] }, { "page": "getChannel", "title": "returns the channel with more than one peak present. It returns NA if there is only one peak present.", "topics": [ "getChannel" ] }, { "page": "ggpairsDens", "title": "produces a scatter plot of the expression matrix of the flowframe. If a cluster variable is given, it assigns different colors to the clusters.", "topics": [ "ggpairsDens" ] }, { "page": "ggplotDens", "title": "plots two channels of a flowframe.", "topics": [ "ggplotDens" ] }, { "page": "ggplotDens2", "title": "plots two channels of a flowframe with different colors for clusters identified.", "topics": [ "ggplotDens2" ] }, { "page": "goodfcs", "title": "indicates if measurement from a flowfile is good or bad.", "topics": [ "goodFcs" ] }, { "page": "is.DebrisFilter", "title": "function to check if object is of class cyanoFilter(DebrisFilter)", "topics": [ "is.DebrisFilter" ] }, { "page": "is.flowFrame", "title": "function to check if object is a flowFrame", "topics": [ "is.flowFrame" ] }, { "page": "is.flowSet", "title": "function to check if object is a flowSet", "topics": [ "is.flowSet" ] }, { "page": "is.MarginEvents", "title": "function to check if object is of class cyanoFilter(MarginEvents)", "topics": [ "is.MarginEvents" ] }, { "page": "is.PhytopFilter", "title": "function to check if object is of class cyanoFilter(PhytoFilter)", "topics": [ "is.PhytopFilter" ] }, { "page": "lnTrans", "title": "log transforms the expression matrix of a flowframe", "topics": [ "lnTrans" ] }, { "page": "MarginEvents", "title": "the marginEvent class", "topics": [ "MarginEvents" ] }, { "page": "newFlowframe", "title": "takes a flowframe, a group indicator and formulates another flowframe with group indicator as part of the expression matrix of the new flowframe.", "topics": [ "newFlowframe" ] }, { "page": "nona", "title": "Removes NA values from the expression matrix of a flow cytometer file.", "topics": [ "noNA" ] }, { "page": "noneg", "title": "Removes negative values from the expression matrix", "topics": [ "noNeg" ] }, { "page": "oneDgate", "title": "returns the labels stating the cluster of each row in a flowfile.", "topics": [ "oneDgate" ] }, { "page": "pairsPlot", "title": "produces a scatter plot of the expression matrix of a flowframe. Note that, it takes some time to display the plot.", "topics": [ "pairsPlot" ] }, { "page": "PhytoFilter", "title": "gates out and assign indicators to phytoplankton cells based on the expression of measured cell complexity channels.", "topics": [ "phytoFilter" ] }, { "page": "PhytopFilter", "title": "the phytofilter class", "topics": [ "PhytopFilter" ] }, { "page": "pigmentGate", "title": "gates out or assign indicators to phytoplankton cells based on the expression of the measured pigments.", "topics": [ "pigmentGate" ] }, { "page": "plot-DebrisFilter-ANY-method", "title": "plot method for DebrisFilter objects", "topics": [ "plot,DebrisFilter,ANY-method" ] }, { "page": "plot-MarginEvents-ANY-method", "title": "plot method for MarginEvents objects", "topics": [ "plot,MarginEvents,ANY-method" ] }, { "page": "plot-PhytopFilter-ANY-method", "title": "plot method for PhytoFilter objects", "topics": [ "plot,PhytopFilter,ANY-method" ] }, { "page": "reducedFlowframe", "title": "generic function for extracting the full flowframe", "topics": [ "reducedFlowframe" ] }, { "page": "reducedFlowframe-DebrisFilter-method", "title": "accesor method for reduced flowframe (DebrisFilter class)", "topics": [ "reducedFlowframe,DebrisFilter-method" ] }, { "page": "reducedFlowframe-MarginEvents-method", "title": "accesor method for reduced flowframe (MarginEvent class)", "topics": [ "reducedFlowframe,MarginEvents-method" ] }, { "page": "reducedFlowframe-PhytopFilter-method", "title": "accesor method for reduced flowframe(PhytoFilter class)", "topics": [ "reducedFlowframe,PhytopFilter-method" ] }, { "page": "retain", "title": "Decides if a file should be retiained or removed based on its status.", "topics": [ "retain" ] }, { "page": "rowNumbers", "title": "returns the position of the cells below, above or between estimated gates", "topics": [ "rowNumbers" ] }, { "page": "summaries", "title": "takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster", "topics": [ "summaries" ] }, { "page": "summaries-DebrisFilter-method", "title": "takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster", "topics": [ "summaries,DebrisFilter-method" ] }, { "page": "summaries-MarginEvents-method", "title": "takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster", "topics": [ "summaries,MarginEvents-method" ] }, { "page": "summaries-PhytopFilter-method", "title": "takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster", "topics": [ "summaries,PhytopFilter-method" ] } ], "_readme": "https://github.com/bioc/cyanoFilter/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "BH", "Biobase", "BiocGenerics", "biocmake", "bitops", "boot", "broom", "car", "carData", "caTools", "cli", "colorspace", "cowplot", "cpp11", "crayon", "cytolib", "cytometree", "deldir", "Deriv", "dir.expiry", "doBy", "dplyr", "farver", "filelock", "flowClust", "flowCore", "flowDensity", "flowViz", "forcats", "forecast", "Formula", "fracdiff", "generics", "geometry", "GGally", "ggplot2", "ggstats", "glue", "GoFKernel", "gplots", "graph", "gtable", "gtools", "hexbin", "hms", "IDPmisc", "igraph", "interp", "isoband", "jpeg", "KernSmooth", "labeling", "lattice", "latticeExtra", "lifecycle", "linprog", "lme4", "lmtest", "lpSolve", "magic", "magrittr", "MASS", "Matrix", "MatrixModels", "matrixStats", "mclust", "mgcv", "microbenchmark", "minqa", "modelr", "mrfDepth", "nlme", "nloptr", "nnet", "numDeriv", "patchwork", "pbkrtest", "pillar", "pkgconfig", "plyr", "png", "polyclip", "prettyunits", "progress", "purrr", "quantreg", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppProgress", "Rdpack", "reformulas", "reshape2", "Rhdf5lib", "rlang", "RProtoBufLib", "S4Vectors", "S7", "scales", "SparseM", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "timeDate", "urca", "utf8", "vctrs", "viridisLite", "withr", "zoo" ], "_vignettes": [ { "source": "cyanoFilter.Rmd", "filename": "cyanoFilter.html", "title": "cyanoFilter", "author": "Olusoji O. 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