{ "_id": "6ae760d09ceaa78f20099f0f", "Package": "flowBeads", "Type": "Package", "Version": "1.51.0", "Title": "flowBeads: Analysis of flow bead data", "Author": "Nikolas Pontikos", "Date": "2013-03-01", "Description": "This package extends flowCore to provide functionality\nspecific to bead data. One of the goals of this package is to\nautomate analysis of bead data for the purpose of\nnormalisation.", "Maintainer": "Nikolas Pontikos ", "License": "Artistic-2.0", "Packaged": { "Date": "2026-11-01 13:35:27 UTC", "User": "root" }, "InstallableEverywhere": "yes", "Collate": "'AllGenerics.R' 'AllClasses.R' 'get-methods.R'\n'show-methods.R' 'plot-methods.R' 'beads.R' 'beads1-data.R'\n'beads2-data.R' 'dakomef-data.R' 'cytocalmef-data.R'\n'flowBeads-package.R'", "biocViews": "ImmunoOncology, Infrastructure, FlowCytometry,\nCellBasedAssays", "Config/pak/sysreqs": "libssl-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:37:46 UTC", "RemoteUrl": "https://github.com/bioc/flowBeads", "RemoteRef": "HEAD", "RemoteSha": "268fcb0d3bcb9105343c023564940ee9fe087233", "NeedsCompilation": "no", "_user": "bioc", "_type": "src", "_file": "flowBeads_1.51.0.tar.gz", "_fileid": "https://r2.ropensci.org/65fb36ecaef3fe3c4b4c3892ca4708816af7bbba1465076f2954f28f5f8ba8e9", "_filesize": 982384, "_sha256": "65fb36ecaef3fe3c4b4c3892ca4708816af7bbba1465076f2954f28f5f8ba8e9", "_expires": "2027-02-09T15:54:54.000Z", "_created": "2026-11-01T13:35:27.000Z", "_published": "2026-11-01T15:54:55.875Z", "_upstream": "https://github.com/bioc/flowBeads", "_status": "success", "_maintainer": { "name": "Nikolas Pontikos", "email": "n.pontikos@gmail.com", "login": "pontikos", "linkedin": "in/nikolaspontikos", "orcid": "0000-0003-1782-4711", "twitter": "@npontikos", "description": "associate prof @ UCL | founder @ Eye2Gene | exited founder @ Phenopolis | ex deputy director @ Moorfields Reading Centre", "uuid": 3852020 }, "_jobs": [ { "job": 124864219029, "time": 137, "config": "bioc-checks", "r": "4.6.2", "check": "FAILURE", "artifact": "" }, { "job": 124864219040, "time": 220, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "13086831106" }, { "job": 124864219060, "time": 234, "config": "linux-release-x86_64", "r": "4.6.2", "check": "WARNING", "artifact": "13087025846" }, { "job": 124864219023, "time": 151, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "13090501709" }, { "job": 124864219086, "time": 91, "config": "macos-release-arm64", "r": "4.6.2", "check": "WARNING", "artifact": "13090945061" }, { "job": 124859383042, "time": 184, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13086340352" }, { "job": 124864219073, "time": 105, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13087070006" }, { "job": 124864219135, "time": 127, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "13085881503" }, { "job": 124864219048, "time": 116, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "13085996341" }, { "job": 124864219103, "time": 104, "config": "windows-release-x86_64", "r": "4.6.2", "check": "WARNING", "artifact": "13086156065" } ], "_buildurl": "https://github.com/r-universe/bioc/actions/runs/41309818123", "_commit": { "id": "268fcb0d3bcb9105343c023564940ee9fe087233", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379866 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.15.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "rrcov", "role": "Depends" }, { "package": "flowCore", "role": "Depends" }, { "package": "flowCore", "role": "Imports" }, { "package": "rrcov", "role": "Imports" }, { "package": "knitr", "role": "Imports" }, { "package": "xtable", "role": "Imports" }, { "package": "flowViz", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.51.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.50.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "immunooncology", "infrastructure", "flowcytometry", "cellbasedassays" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 482, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 667, "source": "https://www.bioconductor.org/packages/stats/bioc/flowBeads" }, "_searchresults": 12, "_abi": { "exports": [ { "key": "flowBeads::BeadFlowFrame", "hash": "ff930306c0688bc0" }, { "key": "flowBeads::GatedBeadFlowFrame", "hash": "0fea12c93c70564b" }, { "key": "flowBeads::generic:absoluteNormalise", "hash": "54a16fb5e875249b" }, { "key": "flowBeads::generic:gateBeads", "hash": "fb09cf7c85103b38" }, { "key": "flowBeads::generic:generateReport", "hash": "8cd802053a00d82e" }, { "key": "flowBeads::generic:getClusteringStats", "hash": "56395c1c212aad8b" }, { "key": "flowBeads::generic:getDate", "hash": "56c385e2fe46dc71" }, { "key": "flowBeads::generic:getMEFparams", "hash": "1d2fd845e0e05344" }, { "key": "flowBeads::generic:getMEFtransform", "hash": "1d6fdb92f714d7d5" }, { "key": "flowBeads::generic:getParams", "hash": "bbca0b89cb66a130" }, { "key": "flowBeads::generic:getTransformFunction", "hash": "96c6dc3a132ea2c1" }, { "key": "flowBeads::generic:hasMEF", "hash": "53f3ce311c8620f8" }, { "key": "flowBeads::generic:relativeNormalise", "hash": "1e539f0c56823a87" }, { "key": "flowBeads::generic:toMEF", "hash": "241559b59edac20b" } ], "imports": [ { "key": "flowCore::flowFrame", "hash": "d6faa7b6eaa633fb" } ] }, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/flowBeads.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "absoluteNormalise", "BeadFlowFrame", "gateBeads", "generateReport", "getClusteringStats", "getDate", "getMEFparams", "getMEFtransform", "getParams", "getTransformFunction", "hasMEF", "mefTransform", "plot", "relativeNormalise", "toMEF" ], "_datasets": [ { "name": "beads1", "title": "Dako beads on day 1", "object": "beads1", "file": "beads1.rda", "class": [ "BeadFlowFrame" ], "fields": [], "table": false, "tojson": false }, { "name": "beads2", "title": "Dako beads on day 2", "object": "beads2", "file": "beads2.rda", "class": [ "BeadFlowFrame" ], "fields": [], "table": false, "tojson": false }, { "name": "cytocalmef", "title": "Cytocal config file", "object": "cytocalmef", "file": "cytocalmef.csv.gz", "class": [ "data.frame" ], "fields": [ "FITC", "PE", "PE.TEXAS.RED", "PERCP.CY5.5", "PE.CY5", "PE.CY7", "APC", "ALEXA.700", "APC.CY7", "PACIFIC.BLUE", "PACIFIC.ORANGE" ], "rows": 6, "table": true, "tojson": true }, { "name": "dakomef", "title": "Dako config file", "object": "dakomef", "file": "dakomef.csv.gz", "class": [ "data.frame" ], "fields": [ "FITC", "PE", "PE.CY5", "APC", "PE.TEXAS.RED" ], "rows": 6, "table": true, "tojson": true } ], "_help": [ { "page": "flowBeads-package", "title": "flowBeads", "topics": [ "flowBeads-package", "flowBeads" ] }, { "page": "absoluteNormalise-methods", "title": "absoluteNormalise", "topics": [ "absoluteNormalise", "absoluteNormalise,GatedBeadFlowFrame,data.frame-method" ] }, { "page": "BeadFlowFrame-class", "title": "BeadFlowFrame", "topics": [ "BeadFlowFrame", "BeadFlowFrame-class", "dBeadFlowFrame" ] }, { "page": "beads1", "title": "Dako beads on day 1", "topics": [ "beads1" ] }, { "page": "beads2", "title": "Dako beads on day 2", "topics": [ "beads2" ] }, { "page": "cytocalmef", "title": "Cytocal config file", "topics": [ "cytocalmef" ] }, { "page": "dakomef", "title": "Dako config file", "topics": [ "dakomef" ] }, { "page": "gateBeads-methods", "title": "gateBeads", "topics": [ "gateBeads", "gateBeads,BeadFlowFrame-method" ] }, { "page": "GatedBeadFlowFrame-class", "title": "GatedBeadFlowFrame", "topics": [ "GatedBeadFlowFrame", "GatedBeadFlowFrame-class" ] }, { "page": "generateReport-methods", "title": "generateReport", "topics": [ "generateReport", "generateReport,GatedBeadFlowFrame,character-method" ] }, { "page": "getClusteringStats-methods", "title": "getClusteringStats", "topics": [ "getClusteringStats", "getClusteringStats,GatedBeadFlowFrame-method" ] }, { "page": "getDate-methods", "title": "getDate", "topics": [ "getDate", "getDate,flowFrame-method" ] }, { "page": "getMEFparams-methods", "title": "getMEFparams", "topics": [ "getMEFparams", "getMEFparams,BeadFlowFrame-method" ] }, { "page": "getMEFtransform-methods", "title": "getMEFtransform", "topics": [ "getMEFtransform", "getMEFtransform,GatedBeadFlowFrame-method" ] }, { "page": "getParams-methods", "title": "getParams", "topics": [ "getParams", "getParams,flowFrame-method" ] }, { "page": "getTransformFunction-methods", "title": "getTransformFunction", "topics": [ "getTransformFunction", "getTransformFunction,BeadFlowFrame-method" ] }, { "page": "hasMEF-methods", "title": "hasMEF", "topics": [ "hasMEF", "hasMEF,BeadFlowFrame,character-method" ] }, { "page": "length-methods", "title": "length", "topics": [ "length", "length,flowFrame-method" ] }, { "page": "mefTransform", "title": "Logicle transformation constructor", "topics": [ "mefTransform" ] }, { "page": "plot-methods", "title": "Plot the results of the clustering. Plot only the requested channel which should have a corresponding entry in the MEF files", "topics": [ "plot", "plot,BeadFlowFrame,character-method", "plot,BeadFlowFrame,missing-method", "plot,GatedBeadFlowFrame,character-method" ] }, { "page": "relativeNormalise-methods", "title": "relativeNormalise", "topics": [ "relativeNormalise", "relativeNormalise,GatedBeadFlowFrame,GatedBeadFlowFrame-method" ] }, { "page": "show-methods", "title": "BeadFlowFrame", "topics": [ "show" ] }, { "page": "toMEF-methods", "title": "toMEF", "topics": [ "toMEF", "toMEF,GatedBeadFlowFrame,flowFrame-method" ] } ], "_readme": "https://github.com/bioc/flowBeads/raw/HEAD/README.md", "_rundeps": [ "BH", "Biobase", "BiocGenerics", "biocmake", "cpp11", "cytolib", "DEoptimR", "dir.expiry", "evaluate", "filelock", "flowCore", "generics", "highr", "knitr", "lattice", "matrixStats", "mvtnorm", "pcaPP", "Rcpp", "Rhdf5lib", "robustbase", "RProtoBufLib", "rrcov", "S4Vectors", "xfun", "xtable", "yaml" ], "_vignettes": [ { "source": "HowTo-flowBeads.Rnw", "filename": "HowTo-flowBeads.pdf", "title": "Analysis of Flow Cytometry Bead Data", "engine": "utils::Sweave", "headings": [ "Theory", "Loading Bead Files", "Gating Bead Data", "Relative Normalisation", "Generating a Report" ], "created": "2013-06-13 21:33:24", "modified": "2013-06-13 21:33:24", "commits": 1 } ], "_score": 4.079181246047625, "_indexed": true, "_nocasepkg": "flowbeads", "_universes": [ "bioc", "pontikos" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.51.0", "date": "2026-11-01T14:08:20.000Z", "distro": "resolute", "commit": "268fcb0d3bcb9105343c023564940ee9fe087233", "fileid": "https://r2.ropensci.org/382068e3c3e5a8854fde8ab248b0a1ba54dfa6c2669ddae71c801c7b49ad9a05", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309818123" }, { "r": "4.6.2", "os": "linux", "version": "1.51.0", "date": "2026-11-01T14:08:44.000Z", "distro": "resolute", "commit": "268fcb0d3bcb9105343c023564940ee9fe087233", "fileid": "https://r2.ropensci.org/46cd9709477a2e6065f2ee5252137b00183edc2485570c28a3f4394345abc474", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309818123" }, { "r": "4.5.3", "os": "mac", "version": "1.51.0", "date": "2026-11-01T15:53:56.000Z", "commit": "268fcb0d3bcb9105343c023564940ee9fe087233", "fileid": "https://r2.ropensci.org/7b4c322ae68313665bd9bcd8cb2bac9ef8b4df837aad3d0c1e2ce7db7f4de512", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309818123" }, { "r": "4.6.2", "os": "mac", "version": "1.51.0", "date": "2026-11-01T15:53:09.000Z", "commit": "268fcb0d3bcb9105343c023564940ee9fe087233", "fileid": "https://r2.ropensci.org/3e0330d7ce3f1e6dc2429b6ce5d1fccbee62a609fb72ccf7606e27e90aed698d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309818123" }, { "r": "4.6.0", "os": "wasm", "version": "1.51.0", "date": "2026-11-01T14:07:18.000Z", "commit": "268fcb0d3bcb9105343c023564940ee9fe087233", "fileid": "https://r2.ropensci.org/c1b474bc185dc20b811d7e457bcd3ff6a6724ca2249d45578597071f34336e29", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309818123" }, { "r": "4.7.0", "os": "win", "version": "1.51.0", "date": "2026-11-01T13:42:46.000Z", "commit": "268fcb0d3bcb9105343c023564940ee9fe087233", "fileid": "https://r2.ropensci.org/4f3e323331687568817e37e8bda3ec11127f132432f8704d49afa8f4b64da5b3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309818123" }, { "r": "4.5.3", "os": "win", "version": "1.51.0", "date": "2026-11-01T13:42:35.000Z", "commit": "268fcb0d3bcb9105343c023564940ee9fe087233", "fileid": "https://r2.ropensci.org/af81e66529e906bf15ec6f83858cd38d9e161addc170c91dd3733aa9fed06ebe", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309818123" }, { "r": "4.6.2", "os": "win", "version": "1.51.0", "date": "2026-11-01T13:42:30.000Z", "commit": "268fcb0d3bcb9105343c023564940ee9fe087233", "fileid": "https://r2.ropensci.org/bcf2a5412a591242a475b21bdd87a47c10de835a7e643e3213fd3c12f0b04cc7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/41309818123" } ] }