{ "_id": "6a3635693efcd9bda43f77a9", "Package": "MetaCyto", "Type": "Package", "Title": "MetaCyto: A package for meta-analysis of cytometry data", "Version": "1.34.0", "Author": "Zicheng Hu, Chethan Jujjavarapu, Sanchita Bhattacharya, Atul J.\nButte", "Maintainer": "Zicheng Hu ", "Description": "This package provides functions for preprocessing,\nautomated gating and meta-analysis of cytometry data. It also\nprovides functions that facilitate the collection of cytometry\ndata from the ImmPort database.", "License": "GPL (>= 2)", "RoxygenNote": "6.0.1", "VignetteBuilder": "knitr, rmarkdown", "biocViews": "ImmunoOncology, CellBiology, FlowCytometry, Clustering,\nStatisticalMethod, Software, CellBasedAssays, Preprocessing", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibglpk-dev make libicu-dev libxml2-dev libssl-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:46:50 UTC", "RemoteUrl": "https://github.com/bioc/MetaCyto", "RemoteRef": "RELEASE_3_23", "RemoteSha": "0eb2b3009d3d16d039f2b59f30040442e68c9741", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-20 06:30:47 UTC", "User": "root" }, "MD5sum": "a25b8c822c7aceb9d00bed87f67a3a27", "_user": "bioc-release", "_type": "src", "_file": "MetaCyto_1.34.0.tar.gz", "_fileid": "1965c4380b50295f34f54bac9b237309580ade661fd1f3dc0de7f2cace7ad85b", "_filesize": 1359687, "_sha256": "1965c4380b50295f34f54bac9b237309580ade661fd1f3dc0de7f2cace7ad85b", "_created": "2026-06-20T06:30:47.000Z", "_published": "2026-06-20T06:38:33.794Z", "_jobs": [ { "job": 82462002729, "time": 190, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7762848927" }, { "job": 82462002783, "time": 422, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7762878608" }, { "job": 82462002748, "time": 358, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7762870282" }, { "job": 82462002765, "time": 245, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7762855931" }, { "job": 82462002751, "time": 241, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7762855527" }, { "job": 82461640687, "time": 361, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7762825061" }, { "job": 82462002737, "time": 153, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7762843686" }, { "job": 82462002806, "time": 407, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7762876791" }, { "job": 82462002793, "time": 376, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7762872946" }, { "job": 82462002787, "time": 351, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7762869476" } ], "_bioccheck": { "error": 2, "warning": 2, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27862817787", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/MetaCyto", "_commit": { "id": "0eb2b3009d3d16d039f2b59f30040442e68c9741", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380410 }, "_maintainer": { "name": "Zicheng Hu", "email": "zicheng.hu@ucsf.edu" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4", "role": "Depends" }, { "package": "flowCore", "version": ">= 1.4", "role": "Imports" }, { "package": "tidyr", "version": ">= 0.7", "role": "Imports" }, { "package": "fastcluster", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "metafor", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "FlowSOM", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.35.0", "bioc": "3.24" }, { "branch": "release", "version": "1.34.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "cellbiology", "flowcytometry", "clustering", "statisticalmethod", "software", "cellbasedassays", "preprocessing" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 440, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 3, "_searchresults": 20, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MetaCyto.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "autoCluster.batch", "clusterStats", "collectData", "densityPlot", "fcsInfoParser", "filterLabels", "findCutoff", "flowHC", "flowSOM.MC", "glmAnalysis", "labelCluster", "labelSummary", "markerFinder", "metaAnalysis", "nameUpdator", "panelSummary", "plotGA", "preprocessing", "preprocessing.batch", "sampleInfoParser", "searchCluster", "searchCluster.batch", "set2Frame" ], "_help": [ { "page": "autoCluster.batch", "title": "Cluster the preprocessed fcs files from different studies in batch", "topics": [ "autoCluster.batch" ] }, { "page": "clusterStats", "title": "Derive summary statistics for clusters", "topics": [ "clusterStats" ] }, { "page": "collectData", "title": "Collect and combine data from multiple csv files of the same format", "topics": [ "collectData" ] }, { "page": "densityPlot", "title": "Draw density plot for each cell cluster.", "topics": [ "densityPlot" ] }, { "page": "fcsInfoParser", "title": "Organize fcs files in a study from ImmPort into panels", "topics": [ "fcsInfoParser" ] }, { "page": "filterLabels", "title": "Filter cluster labels", "topics": [ "filterLabels" ] }, { "page": "findCutoff", "title": "Find cutoff for a 1D distribution", "topics": [ "findCutoff" ] }, { "page": "flowHC", "title": "Cluster cytometry data using hierarchical clustering", "topics": [ "flowHC" ] }, { "page": "flowSOM.MC", "title": "Cluster cytometry data using FlowSOM", "topics": [ "flowSOM.MC" ] }, { "page": "glmAnalysis", "title": "Perform generalized linear model analysis to estimate effect size.", "topics": [ "glmAnalysis" ] }, { "page": "labelCluster", "title": "Label each cluster as \"+\" or \"-\" or neutral for each marker", "topics": [ "labelCluster" ] }, { "page": "labelSummary", "title": "Make a summary for the labels (cell populations) identified in different cytometry panels.", "topics": [ "labelSummary" ] }, { "page": "markerFinder", "title": "Find markers in a flow frame object", "topics": [ "markerFinder" ] }, { "page": "metaAnalysis", "title": "Performs meta-analysis", "topics": [ "metaAnalysis" ] }, { "page": "nameUpdator", "title": "Used to update marker names", "topics": [ "nameUpdator" ] }, { "page": "panelSummary", "title": "Summarize markers in panels.", "topics": [ "panelSummary" ] }, { "page": "plotGA", "title": "Plot the result from the glmAnalysis function", "topics": [ "plotGA" ] }, { "page": "preprocessing", "title": "Preprocess fcs files from a single experiment", "topics": [ "preprocessing" ] }, { "page": "preprocessing.batch", "title": "Preprocessing fcs files from different studies in batch.", "topics": [ "preprocessing.batch" ] }, { "page": "sampleInfoParser", "title": "Collect sample information for fcs files in a study from ImmPort.", "topics": [ "sampleInfoParser" ] }, { "page": "searchCluster", "title": "Search for clusters using pre-defined labels", "topics": [ "searchCluster" ] }, { "page": "searchCluster.batch", "title": "Search for clusters using pre-defined labels in cytometry data from different studies in batch", "topics": [ "searchCluster.batch" ] }, { "page": "set2Frame", "title": "Combine cells in a flow set into a flow frame.", "topics": [ "set2Frame" ] } ], "_readme": "https://github.com/bioc/MetaCyto/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "ALL", "backports", "base64enc", "BH", "Biobase", "BiocGenerics", "biocmake", "boot", "broom", "car", "carData", "cli", "cluster", "colorRamps", "colorspace", "ConsensusClusterPlus", "corrplot", "cowplot", "cpp11", "cytolib", "Deriv", "digest", "dir.expiry", "doBy", "dplyr", "farver", "fastcluster", "filelock", "flowCore", "FlowSOM", "forecast", "Formula", "fracdiff", "generics", "ggforce", "ggnewscale", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "glue", "gridExtra", "gtable", "igraph", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "mathjaxr", "Matrix", "MatrixModels", "matrixStats", "metadat", "metafor", "mgcv", "microbenchmark", "minqa", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "pbapply", "pbkrtest", "pillar", "pkgconfig", "polyclip", "polynom", "purrr", "quantreg", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "Rhdf5lib", "rlang", "RProtoBufLib", "rstatix", "Rtsne", "S4Vectors", "S7", "scales", "SparseM", "stringi", "stringr", "survival", "systemfonts", "tibble", "tidyr", "tidyselect", "timeDate", "tweenr", "urca", "utf8", "vctrs", "viridisLite", "withr", "XML", "zoo" ], "_vignettes": [ { "source": "MetaCyto_Vignette.Rmd", "filename": "MetaCyto_Vignette.html", "title": "Introduction to MetaCyto", "author": "Zicheng Hu", "engine": "knitr::rmarkdown", "headings": [ "Example 1: Local Cytometry Datasets.", "Step 1: data collection", "Step 2: data preprocessing", "step 3: Identification of common clusters across studies", "Step 4: Statistical analysis", "Example 2: Data collection for ImmPort datasets" ], "created": "2017-04-20 16:47:29", "modified": "2018-06-08 17:21:35", "commits": 11 } ], "_score": 4.778151250383644, "_indexed": false, "_nocasepkg": "metacyto", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/MetaCyto", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.34.0", "date": "2026-06-20T06:34:37.000Z", "distro": "noble", "commit": "0eb2b3009d3d16d039f2b59f30040442e68c9741", "fileid": "271e835a8f3944a2f36488b63246f0586a9e610377222fb8dfa73c344e3d6bc3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27862817787" }, { "r": "4.6.0", "os": "linux", "version": "1.34.0", "date": "2026-06-20T06:34:02.000Z", "distro": "noble", "commit": "0eb2b3009d3d16d039f2b59f30040442e68c9741", "fileid": "c165f936773a024a27b8d641d246d0055cea1634a513a1c839b90fe94a593c8b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27862817787" }, { "r": "4.5.3", "os": "mac", "version": "1.34.0", "date": "2026-06-20T06:32:32.000Z", "commit": "0eb2b3009d3d16d039f2b59f30040442e68c9741", "fileid": "31eaef8c52423de3515b02ca3f8173467d439c69e205a5c8d887a4f2c8c80260", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27862817787" }, { "r": "4.6.0", "os": "mac", "version": "1.34.0", "date": "2026-06-20T06:32:21.000Z", "commit": "0eb2b3009d3d16d039f2b59f30040442e68c9741", "fileid": "5429a4b581699ca8190652dba91b8672708751cd9d4a2ad8335ffba331c6c458", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27862817787" }, { "r": "4.6.0", "os": "wasm", "version": "1.34.0", "date": "2026-06-20T06:33:41.000Z", "commit": "0eb2b3009d3d16d039f2b59f30040442e68c9741", "fileid": "8abacb4e1630702e41b60b0f26948929b54653592485d08d36b79edaa28a583d", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27862817787" }, { "r": "4.7.0", "os": "win", "version": "1.34.0", "date": "2026-06-20T06:32:43.000Z", "commit": "0eb2b3009d3d16d039f2b59f30040442e68c9741", "fileid": "02890bf86ea83fe7e63dac663554d1b0a929ba7a78b784b57676d4fa56dca644", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27862817787" }, { "r": "4.5.3", "os": "win", "version": "1.34.0", "date": "2026-06-20T06:32:43.000Z", "commit": "0eb2b3009d3d16d039f2b59f30040442e68c9741", "fileid": "944020ad406061ea3dc484bf7130c925b2e38cd571c833abc0d7e4dcdd9ebe0e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27862817787" }, { "r": "4.6.0", "os": "win", "version": "1.34.0", "date": "2026-06-20T06:32:34.000Z", "commit": "0eb2b3009d3d16d039f2b59f30040442e68c9741", "fileid": "c138fbd6c73b8e522fb5dd65601f128e8ec00d788bd9cb958aa3f383a9600c93", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27862817787" } ] }