{ "_id": "6a1af13f1d7bb097a09f6f48", "Package": "treekoR", "Type": "Package", "Title": "Cytometry Cluster Hierarchy and Cellular-to-phenotype\nAssociations", "Version": "1.21.0", "Authors@R": "c(person(\"Adam\", \"Chan\", role = c(\"aut\", \"cre\"),\nemail = \"adam.s.chan@sydney.edu.au\"),\nperson(\"Ellis\", \"Patrick\", role = \"ctb\"))", "biocViews": "Clustering, DifferentialExpression, FlowCytometry,\nImmunoOncology, MassSpectrometry, SingleCell, Software,\nStatisticalMethod, Visualization", "Description": "treekoR is a novel framework that aims to utilise the\nhierarchical nature of single cell cytometry data to find\nrobust and interpretable associations between cell subsets and\npatient clinical end points. These associations are aimed to\nrecapitulate the nested proportions prevalent in workflows\ninovlving manual gating, which are often overlooked in\nworkflows using automatic clustering to identify cell\npopulations. We developed treekoR to: Derive a hierarchical\ntree structure of cell clusters; quantify a cell types as a\nproportion relative to all cells in a sample (%total), and, as\nthe proportion relative to a parent population (%parent);\nperform significance testing using the calculated proportions;\nand provide an interactive html visualisation to help highlight\nkey results.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "false", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev perl zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:55:45 UTC", "RemoteUrl": "https://github.com/bioc/treekoR", "RemoteRef": "HEAD", "RemoteSha": "e1ad33cc0dafa3642199c9c99353bd912b2736b7", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:43:11 UTC", "User": "root" }, "Author": "Adam Chan [aut, cre],\nEllis Patrick [ctb]", "Maintainer": "Adam Chan ", "MD5sum": "efb08c86c88817f5e7b7600b670a7bc3", "_user": "bioc", "_type": "src", "_file": "treekoR_1.21.0.tar.gz", "_fileid": "022acf1e2c014285659784c823fc44ccd630a3d55d0b13f8c9a478478042e165", "_filesize": 2010991, "_sha256": "022acf1e2c014285659784c823fc44ccd630a3d55d0b13f8c9a478478042e165", "_created": "2026-05-30T09:43:11.000Z", "_published": "2026-05-30T14:16:31.581Z", "_jobs": [ { "job": 78640446563, "time": 240, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307435273" }, { "job": 78640446573, "time": 472, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307456751" }, { "job": 78640446567, "time": 470, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307456550" }, { "job": 78640446599, "time": 305, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7308797575" }, { "job": 78640446592, "time": 228, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7308789671" }, { "job": 78639704927, "time": 359, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307269177" }, { "job": 78640446548, "time": 207, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307431905" }, { "job": 78640446586, "time": 368, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7307446840" }, { "job": 78640446581, "time": 327, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7307443467" }, { "job": 78640446596, "time": 334, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7307443868" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676459969", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/treekoR", "_commit": { "id": "e1ad33cc0dafa3642199c9c99353bd912b2736b7", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380945 }, "_maintainer": { "name": "Adam Chan", "email": "adam.s.chan@sydney.edu.au", "login": "adam2o1o", "description": "", "uuid": 47180027 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "ggiraph", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "hopach", "role": "Imports" }, { "package": "ape", "role": "Imports" }, { "package": "ggtree", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "diffcyt", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "lme4", "role": "Imports" }, { "package": "multcomp", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "CATALYST", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "clustering", "differentialexpression", "flowcytometry", "immunooncology", "massspectrometry", "singlecell", "software", "statisticalmethod", "visualization" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 405, "source": "https://www.bioconductor.org/packages/stats/bioc/treekoR" }, "_searchresults": 13, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/treekoR.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "colourTree", "getCellGMeans", "getCellProp", "getClusterTree", "getTreeResults", "hopachToPhylo", "plotInteractiveHeatmap", "runHOPACH", "testTree" ], "_datasets": [ { "name": "DeBiasi_COVID_CD8_samp", "title": "COVID-19 Sample data", "object": "COVIDSampleData", "file": "COVIDSampleData.rda", "class": [ "SingleCellExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "addFreqBars", "title": "Title", "topics": [ "addFreqBars" ] }, { "page": "addHeatMap", "title": "Title", "topics": [ "addHeatMap" ] }, { "page": "addTree", "title": "Title", "topics": [ "addTree" ] }, { "page": "colourTree", "title": "colourTree", "topics": [ "colourTree" ] }, { "page": "DeBiasi_COVID_CD8_samp", "title": "COVID-19 Sample data", "topics": [ "DeBiasi_COVID_CD8_samp" ] }, { "page": "findChildren", "title": "findChildren", "topics": [ "findChildren" ] }, { "page": "geometricMean", "title": "geometricMean", "topics": [ "geometricMean" ] }, { "page": "getCellGMeans", "title": "getCellGMeans", "topics": [ "getCellGMeans" ] }, { "page": "getCellProp", "title": "getCellProp", "topics": [ "getCellProp" ] }, { "page": "getClusterTree", "title": "getClusterTree This function takes a CATALYST sce with clusters and creates a hierarchical tree", "topics": [ "getClusterTree" ] }, { "page": "getParentProp", "title": "getParentProp", "topics": [ "getParentProp" ] }, { "page": "getTotalProp", "title": "getTotalProp", "topics": [ "getTotalProp" ] }, { "page": "getTreeResults", "title": "getTreeResults", "topics": [ "getTreeResults" ] }, { "page": "hopachToPhylo", "title": "hopachToPhylo", "topics": [ "hopachToPhylo" ] }, { "page": "plotInteractiveHeatmap", "title": "Title", "topics": [ "plotInteractiveHeatmap" ] }, { "page": "plotSigScatter", "title": "plotSigScatter", "topics": [ "plotSigScatter" ] }, { "page": "runEdgeRTests", "title": "runEdgeRTests", "topics": [ "runEdgeRTests" ] }, { "page": "runGLMMTests", "title": "runGLMMTests", "topics": [ "runGLMMTests" ] }, { "page": "runHOPACH", "title": "runHOPACH", "topics": [ "runHOPACH" ] }, { "page": "testTree", "title": "testTree", "topics": [ "testTree" ] } ], "_readme": "https://github.com/bioc/treekoR/raw/HEAD/README.md", "_rundeps": [ "abind", "ALL", "ape", "aplot", "backports", "base64enc", "BH", "Biobase", "BiocGenerics", "biocmake", "boot", "broom", "bslib", "cachem", "car", "carData", "circlize", "cli", "clue", "cluster", "codetools", "colorRamps", "colorspace", "ComplexHeatmap", "ConsensusClusterPlus", "corrplot", "cowplot", "cpp11", "crayon", "cytolib", "data.table", "DelayedArray", "Deriv", "diffcyt", "digest", "dir.expiry", "doBy", "doParallel", "dplyr", "edgeR", "evaluate", "farver", "fastmap", "filelock", "flowCore", "FlowSOM", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "foreach", "forecast", "Formula", "fracdiff", "fs", "gdtools", "generics", "GenomicRanges", "GetoptLong", "ggforce", "ggfun", "ggiraph", "ggnewscale", "ggplot2", "ggplotify", "ggpubr", "ggrepel", "ggsci", "ggsignif", "ggtree", "GlobalOptions", "glue", "gridExtra", "gridGraphics", "gtable", "highr", "hopach", "htmltools", "htmlwidgets", "igraph", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lazyeval", "lifecycle", "limma", "lme4", "lmtest", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "memoise", "mgcv", "microbenchmark", "mime", "minqa", "modelr", "multcomp", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "patchwork", "pbkrtest", "pillar", "pkgconfig", "plyr", "png", "polyclip", "polynom", "purrr", "quantreg", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "reshape2", "Rhdf5lib", "rjson", "rlang", "rmarkdown", "RProtoBufLib", "rstatix", "Rtsne", "S4Arrays", "S4Vectors", "S7", "sandwich", "sass", "scales", "Seqinfo", "shape", "SingleCellExperiment", "SparseArray", "SparseM", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "systemfonts", "TH.data", "tibble", "tidyr", "tidyselect", "tidytree", "timeDate", "tinytex", "treeio", "tweenr", "urca", "utf8", "vctrs", "viridisLite", "withr", "xfun", "XML", "XVector", "yaml", "yulab.utils", "zoo" ], "_vignettes": [ { "source": "vignette.Rmd", "filename": "vignette.html", "title": "treekoR", "author": "Adam Chan, Ellis Patrick", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Overview", "Usage", "Example Data", "Set up", "Construction of Hierarchy of Clusters", "Significance testing of Cell Subpopulations", "Extracting significance results", "Interactive Visualisation", "Using different hierarchical aggregations", "Using counts models for significance testing", "Feature extraction", "Extracting Proportions", "Extracting Expression Geometric Means" ], "created": "2021-02-02 21:57:59", "modified": "2021-10-26 06:05:45", "commits": 7 } ], "_score": 4.5910646070264995, "_indexed": true, "_nocasepkg": "treekor", "_universes": [ "bioc", "adam2o1o" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-05-30T10:12:48.000Z", "distro": "noble", "commit": "e1ad33cc0dafa3642199c9c99353bd912b2736b7", "fileid": "7f1409db58b895d6b79f2722af7d29bc5b38b6826d5dcdd7321d8955636db741", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676459969" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-05-30T10:13:13.000Z", "distro": "noble", "commit": "e1ad33cc0dafa3642199c9c99353bd912b2736b7", "fileid": "c35e8c14a981413b46b4c747d482ab7dda9c07e752d7b4b75a05dbbc5835a6b6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676459969" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-05-30T14:13:10.000Z", "commit": "e1ad33cc0dafa3642199c9c99353bd912b2736b7", "fileid": "336eb12fef3fc331fc938c97151d00fa1d01b57158851af21f5635d8377b6491", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676459969" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-05-30T14:12:36.000Z", "commit": "e1ad33cc0dafa3642199c9c99353bd912b2736b7", "fileid": "6cc1eb4d91a3998ab4d9203a7392d9ebde3399aa9bd03e514e10c4b2e0cad957", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676459969" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-05-30T10:12:32.000Z", "commit": "e1ad33cc0dafa3642199c9c99353bd912b2736b7", "fileid": "30f1a1fe9c1fcc261adb92c041f1dca59fea4dfdd0bbbcc8396497b8767add8b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676459969" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-05-30T10:11:05.000Z", "commit": "e1ad33cc0dafa3642199c9c99353bd912b2736b7", "fileid": "4ecf707649b297a8109f645a21d62b31cc4811b535610a116667bb93aee3aec9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676459969" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-05-30T10:10:59.000Z", "commit": "e1ad33cc0dafa3642199c9c99353bd912b2736b7", "fileid": "bc937b3c5569b6b3fa91e9371c40d783b6c03bb59b0d7ec627e1fe0d2b34451d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676459969" }, { "r": "4.6.0", "os": "win", "version": "1.21.0", "date": "2026-05-30T10:10:46.000Z", "commit": "e1ad33cc0dafa3642199c9c99353bd912b2736b7", "fileid": "7e518811b7ba5c357351d88ee397569f8c6a82480aab3128702a0d12fcfa19bb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676459969" } ] }