{ "_id": "6abb72c899f7aa8c6aa44380", "Package": "CySA", "Title": "Interactive Cluster Selector for Cytometry Data", "Version": "0.99.28", "Authors@R": "person(\"Bernd\", \"Jagla\", , \"bernd.jagla@pasteur.fr\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-7696-0484\"))", "Description": "CySA provides an interactive Shiny-based tool for\nanalyzing flow and mass cytometry data. It supports\nself-organizing map (SOM) based clustering, dimension reduction\n(t-SNE, UMAP, PCA), and statistical comparison of cell\npopulations across sample groups. Users can select cell\nclusters interactively via 2D scatter plots, dendrograms, or\nSOM node grids, and explore marker expression patterns across\nthe selected populations.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "8.0.0", "biocViews": "SingleCell, FlowCytometry, Clustering, Visualization,\nShinyApps", "URL": "https://github.com/baj12/CySA", "BugReports": "https://github.com/baj12/CySA/issues", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibgdal-dev gdal-bin libgeos-dev libglpk-dev make libicu-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev perl libproj-dev\npython3 libsqlite3-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-08-02 07:34:17 UTC", "RemoteUrl": "https://github.com/bioc/CySA", "RemoteRef": "HEAD", "RemoteSha": "fab459b70225e608bdd7cb18627c68dcd10bd4d0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-29 07:52:28 UTC", "User": "root" }, "Author": "Bernd Jagla [aut, cre] (ORCID: )", "Maintainer": "Bernd Jagla ", "_user": "bioc", "_type": "src", "_file": "CySA_0.99.28.tar.gz", "_fileid": "https://r2.ropensci.org/a59bf03767e0573ea40187e929ce336cc484f1bf7cb3a72b3b7fcb237c108571", "_filesize": 2972598, "_sha256": "a59bf03767e0573ea40187e929ce336cc484f1bf7cb3a72b3b7fcb237c108571", "_expires": "2027-01-07T08:11:50.000Z", "_created": "2026-09-29T07:52:28.000Z", "_published": "2026-09-29T08:11:52.732Z", "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/36538629295", "_status": "success", "_upstream": "https://github.com/bioc/CySA", "_commit": { "id": "fab459b70225e608bdd7cb18627c68dcd10bd4d0", "author": "baj12 ", "committer": "baj12 ", "message": "updated intro with specific flowsom example\n", "time": 1785656057 }, "_maintainer": { "name": "Bernd Jagla", "email": "bernd.jagla@pasteur.fr", "login": "baj12", "description": "", "uuid": 1478035, "orcid": "0000-0002-7696-0484" }, "_distro": "resolute", "_jobs": [ { "job": 109310802236, "time": 290, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11019883186" }, { "job": 109310802138, "time": 1070, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11021180855" }, { "job": 109310802176, "time": 884, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11019997427" }, { "job": 109310802254, "time": 827, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11020965239" }, { "job": 109310802200, "time": 830, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11020760960" }, { "job": 109308600653, "time": 409, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11019493406" }, { "job": 109310802166, "time": 237, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11019883024" }, { "job": 109310802237, "time": 798, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11020496492" }, { "job": 109310802258, "time": 933, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11020566654" }, { "job": 109310802187, "time": 1066, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11020926282" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "shiny", "role": "Imports" }, { "package": "shinydashboard", "role": "Imports" }, { "package": "shinydashboardPlus", "role": "Imports" }, { "package": "shinyjs", "role": "Imports" }, { "package": "shinyjqui", "role": "Imports" }, { "package": "htmltools", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "CATALYST", "role": "Imports" }, { "package": "FlowSOM", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "raster", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "plotly", "role": "Imports" }, { "package": "viridis", "role": "Imports" }, { "package": "dendextend", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "Rtsne", "role": "Imports" }, { "package": "umap", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { "package": "collapsibleTree", "role": "Imports" }, { "package": "withr", "role": "Imports" }, { "package": "KernSmooth", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "jsonlite", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "shinytest2", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-25", "n": 32 }, { "week": "2026-29", "n": 3 }, { "week": "2026-30", "n": 8 }, { "week": "2026-31", "n": 18 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "0.99.28", "bioc": "3.24" } ], "_topics": [ "singlecell", "flowcytometry", "clustering", "visualization", "shinyapps" ], "_stars": 1, "_contributors": [ { "user": "baj12", "count": 66, "uuid": 1478035 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 470, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 218, "source": "https://www.bioconductor.org/packages/stats/bioc/CySA" }, "_devurl": "https://github.com/baj12/cysa", "_searchresults": 0, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/CySA.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_homeurl": "https://github.com/baj12/cysa", "_realowner": "bioc", "_cranurl": false, "_exports": [ "clusterSelector", "CySA_default_cluster_cols", "CySA_example_sce", "plotCytoScatter", "plotSOMScatter", "prepClusterSelector", "prepClusterSelectorData" ], "_help": [ { "page": "clusterSelector", "title": "Cluster Selector Shiny Application", "topics": [ "clusterSelector" ] }, { "page": "CySA_default_cluster_cols", "title": "Default cluster color palette", "topics": [ "CySA_default_cluster_cols" ] }, { "page": "CySA_example_sce", "title": "Minimal example SingleCellExperiment for CySA", "topics": [ "CySA_example_sce" ] }, { "page": "plotCytoScatter", "title": "Plot Scatter for a SingleCellExperiment", "topics": [ "plotCytoScatter" ] }, { "page": "plotSOMScatter", "title": "Scatter plot", "topics": [ "plotSOMScatter" ] }, { "page": "prepClusterSelector", "title": "Prepare Cluster Selector Outputs", "topics": [ "prepClusterSelector" ] }, { "page": "prepClusterSelectorData", "title": "Prepare Data for the Cluster Selector Shiny App", "topics": [ "prepClusterSelectorData" ] } ], "_readme": "https://github.com/bioc/CySA/raw/HEAD/README.md", "_rundeps": [ "abind", "ALL", "askpass", "assorthead", "backports", "base64enc", "beachmat", "beeswarm", "BH", "Biobase", "BiocGenerics", "biocmake", "BiocNeighbors", "BiocParallel", "BiocSingular", "boot", "broom", "bslib", "cachem", "car", "carData", "CATALYST", "circlize", "cli", "clue", "cluster", "codetools", "collapsibleTree", "colorRamps", "colorspace", "commonmark", "ComplexHeatmap", "ConsensusClusterPlus", "corrplot", "cowplot", "cpp11", "crayon", "crosstalk", "curl", "cytolib", "data.table", "data.tree", "DelayedArray", "dendextend", "Deriv", "digest", "dir.expiry", "doBy", "doParallel", "dplyr", "dqrng", "drc", "DT", "evaluate", "farver", "fastmap", "filelock", "flowCore", "FlowSOM", "FNN", "fontawesome", "foreach", "forecast", "formatR", "Formula", "fracdiff", "fresh", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "GetoptLong", "ggbeeswarm", "ggforce", "ggnewscale", "ggplot2", "ggpubr", "ggrepel", "ggridges", "ggsci", "ggsignif", "GlobalOptions", "glue", "gridExtra", "gtable", "gtools", "here", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "igraph", "IRanges", "irlba", "isoband", "iterators", "jquerylib", "jsonlite", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "memoise", "mgcv", "mime", "minqa", "modelr", "multcomp", "mvtnorm", "nlme", "nloptr", "nnet", "nnls", "numDeriv", "openssl", "otel", "pbkrtest", "pheatmap", "pillar", "pkgconfig", "plotly", "plotrix", "plyr", "png", "polyclip", "polynom", "promises", "purrr", "quantreg", "R6", "rappdirs", "raster", "rbibutils", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppML", "RcppProgress", "RcppTOML", "Rdpack", "reformulas", "reshape2", "reticulate", "Rhdf5lib", "rjson", "rlang", "rmarkdown", "rprojroot", "RProtoBufLib", "RSpectra", "rstatix", "rstudioapi", "rsvd", "Rtsne", "S4Arrays", "S4Vectors", "S7", "sandwich", "sass", "ScaledMatrix", "scales", "scater", "scuttle", "Seqinfo", "shape", "shiny", "shinydashboard", "shinydashboardPlus", "shinyjqui", "shinyjs", "SingleCellExperiment", "sitmo", "snow", "sourcetools", "sp", "SparseArray", "SparseM", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "systemfonts", "terra", "TH.data", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "tweenr", "umap", "urca", "utf8", "uwot", "vctrs", "vipor", "viridis", "viridisLite", "waiter", "withr", "xfun", "XML", "xtable", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "intro.Rmd", "filename": "intro.html", "title": "Introduction to CySA", "author": "Bernd Jagla, Institut Pasteur", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Installation", "Quick start", "FlowSOM preprocessing workflow", "Data preprocessing", "Running FlowSOM", "Preparing FlowSOM output for CySA", "Building CySA inputs from FlowSOM output", "Troubleshooting Summary", "Statistical comparison", "Static plots", "Related cytometry workflows", "Session information" ], "created": "2026-06-19 10:48:09", "modified": "2026-08-02 07:34:17", "commits": 10 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "cysa", "_universes": [ "bioc", "baj12" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.28", "date": "2026-09-29T07:57:46.000Z", "distro": "resolute", "commit": "fab459b70225e608bdd7cb18627c68dcd10bd4d0", "fileid": "https://r2.ropensci.org/b7c6dbb20af125a3e9fbd0ac139b5eb68f5cfa241b50238b34343c1e31050909", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36538629295" }, { "r": "4.6.1", "os": "linux", "version": "0.99.28", "date": "2026-09-29T07:57:35.000Z", "distro": "resolute", "commit": "fab459b70225e608bdd7cb18627c68dcd10bd4d0", "fileid": "https://r2.ropensci.org/7b48c8af1507839cf222fb11fd29efd58b52a36bf06e3b5777a63f470ccc27c2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36538629295" }, { "r": "4.5.3", "os": "mac", "version": "0.99.28", "date": "2026-09-29T07:55:22.000Z", "commit": "fab459b70225e608bdd7cb18627c68dcd10bd4d0", "fileid": "https://r2.ropensci.org/e4fb5cb9e5f2b1b4cd1e9ea78c423155c2a9806a18f9c0e052880ed51bcfdca3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36538629295" }, { "r": "4.6.1", "os": "mac", "version": "0.99.28", "date": "2026-09-29T07:55:07.000Z", "commit": "fab459b70225e608bdd7cb18627c68dcd10bd4d0", "fileid": "https://r2.ropensci.org/bd7992bafeb467eef704eec5dcf1d376058e1f6856e0ab8f0f4c7cc33d5ecaa3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36538629295" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.28", "date": "2026-09-29T07:57:19.000Z", "commit": "fab459b70225e608bdd7cb18627c68dcd10bd4d0", "fileid": "https://r2.ropensci.org/c542bf1827d8ac1efcc315f4dd613fd813d0c0211ab536824fb9c4e44598f39f", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36538629295" }, { "r": "4.7.0", "os": "win", "version": "0.99.28", "date": "2026-09-29T07:56:16.000Z", "commit": "fab459b70225e608bdd7cb18627c68dcd10bd4d0", "fileid": "https://r2.ropensci.org/9281f48e563a2108e0d028e5c10e61871e99a449337cd5eaa86ff38ccbc4f6dd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36538629295" }, { "r": "4.5.3", "os": "win", "version": "0.99.28", "date": "2026-09-29T07:56:02.000Z", "commit": "fab459b70225e608bdd7cb18627c68dcd10bd4d0", "fileid": "https://r2.ropensci.org/f625b7e50ce3f93d54756b6296dc79009adf02c5e03a0ecf743124a27506548f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36538629295" }, { "r": "4.6.1", "os": "win", "version": "0.99.28", "date": "2026-09-29T07:55:29.000Z", "commit": "fab459b70225e608bdd7cb18627c68dcd10bd4d0", "fileid": "https://r2.ropensci.org/18115007d17099cef9e257954c0cc9292ef4cc3c4ded5196b3fda0d837cb8a55", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/36538629295" } ] }