{ "_id": "6ae5ee2995ca2370cc8d2222", "Package": "cytofWorkflow", "Title": "CyTOF workflow: differential discovery in high-throughput\nhigh-dimensional cytometry datasets", "Version": "1.37.0", "Date": "2023-10-28", "Authors@R": "c(\nperson(role=c(\"aut\"), \"Malgorzata\", \"Nowicka\", email = \"gosia.nowicka.uzh@gmail.com\"),\nperson(role=\"aut\", \"Helena L.\", \"Crowell\", email = \"helena@crowell.eu\"),\nperson(role=c(\"aut\", \"cre\"), \"Mark D.\", \"Robinson\", email = \"mark.robinson@mls.uzh.ch\"))", "Description": "High-dimensional mass and flow cytometry (HDCyto)\nexperiments have become a method of choice for high-throughput\ninterrogation and characterization of cell populations. Here,\nwe present an updated R-based pipeline for differential\nanalyses of HDCyto data, largely based on Bioconductor\npackages. We computationally define cell populations using\nFlowSOM clustering, and facilitate an optional but reproducible\nstrategy for manual merging of algorithm-generated clusters.\nOur workflow offers different analysis paths, including\nassociation of cell type abundance with a phenotype or changes\nin signaling markers within specific subpopulations, or\ndifferential analyses of aggregated signals. Importantly, the\ndifferential analyses we show are based on regression\nframeworks where the HDCyto data is the response; thus, we are\nable to model arbitrary experimental designs, such as those\nwith batch effects, paired designs and so on. In particular, we\napply generalized linear mixed models or linear mixed models to\nanalyses of cell population abundance or\ncell-population-specific analyses of signaling markers,\nallowing overdispersion in cell count or aggregated signals\nacross samples to be appropriately modeled. To support the\nformal statistical analyses, we encourage exploratory data\nanalysis at every step, including quality control (e.g.,\nmulti-dimensional scaling plots), reporting of clustering\nresults (dimensionality reduction, heatmaps with dendrograms)\nand differential analyses (e.g., plots of aggregated signals).", "License": "Artistic-2.0", "Encoding": "UTF-8", "biocViews": "ImmunoOncologyWorkflow, Workflow, SingleCellWorkflow", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Workflow": "true", "URL": "https://github.com/markrobinsonuzh/cytofWorkflow", "BugReports": "https://github.com/markrobinsonuzh/cytofWorkflow/issues", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibglpk-dev make libicu-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev perl zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:40:24 UTC", "RemoteUrl": "https://github.com/bioc/cytofWorkflow", "RemoteRef": "HEAD", "RemoteSha": "bd00dfcf2284b72b718d1761dfa241650155f6d4", "Packaged": { "Date": "2026-10-31 12:08:15 UTC", "User": "root" }, "Author": "Malgorzata Nowicka [aut],\nHelena L. Crowell [aut],\nMark D. Robinson [aut, cre]", "Maintainer": "Mark D. Robinson ", "_user": "bioc", "_type": "src", "_file": "cytofWorkflow_1.37.0.tar.gz", "_fileid": "https://r2.ropensci.org/9945a0310e9f5bfa76b79f26a557e8ac228b78ce15ebb66a74c1c67e65a4d3f8", "_filesize": 100218, "_sha256": "9945a0310e9f5bfa76b79f26a557e8ac228b78ce15ebb66a74c1c67e65a4d3f8", "_expires": "2027-02-08T13:33:27.000Z", "_created": "2026-10-31T12:08:15.000Z", "_published": "2026-10-31T13:33:29.157Z", "_upstream": "https://github.com/bioc/cytofWorkflow", "_status": "failure", "_maintainer": { "name": "Mark D. Robinson", "email": "mark.robinson@mls.uzh.ch", "login": "markrobinsonuzh", "linkedin": "in/mark-robinson-976620", "twitter": "@markrobinsonca", "description": "Full Professor for Statistical Genomics at University of Zurich", "uuid": 6471769 }, "_jobs": [ { "job": 124533189209, "time": 214, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "13041799085" }, { "job": 124533189126, "time": 277, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "13041869062" }, { "job": 124533189115, "time": 274, "config": "linux-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "13042341448" }, { "job": 124533189123, "time": 152, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "13044244160" }, { "job": 124533189119, "time": 149, "config": "macos-release-arm64", "r": "4.6.2", "check": "ERROR", "artifact": "13043929909" }, { "job": 124532132835, "time": 300, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": 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