{ "_id": "6a195661acfb0bcc41de1df3", "Package": "infinityFlow", "Title": "Augmenting Massively Parallel Cytometry Experiments Using\nMultivariate Non-Linear Regressions", "Version": "1.22.0", "Authors@R": "c(\nperson(\"Etienne\",\"Becht\",middle=NULL,email=\"etienne.becht@protonmail.com\",role=c(\"cre\",\"aut\"))\n)", "Description": "Pipeline to analyze and merge data files produced by\nBioLegend's LEGENDScreen or BD Human Cell Surface Marker\nScreening Panel (BD Lyoplates).", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "false", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.2", "biocViews": "Software, FlowCytometry, CellBasedAssays, SingleCell,\nProteomics", "Config/pak/sysreqs": "libgdal-dev gdal-bin libgeos-dev make libpng-dev\nlibproj-dev libsqlite3-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:53:12 UTC", "RemoteUrl": "https://github.com/bioc/infinityFlow", "RemoteRef": "RELEASE_3_23", "RemoteSha": "aebfdae58d1a58c1bd01a700bd36b41c1bdd9780", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:48:44 UTC", "User": "root" }, "Author": "Etienne Becht [cre, aut]", "Maintainer": "Etienne Becht ", "MD5sum": "4932ba31cb7b9cc060e6d98cfe9fe776", "_user": "bioc-release", "_type": "src", "_file": "infinityFlow_1.22.0.tar.gz", "_fileid": "c41d5076de4374b52e1f6d2f5a4c4a760a7dac8c5ac9b26de27051881586caf5", "_filesize": 1904838, "_sha256": "c41d5076de4374b52e1f6d2f5a4c4a760a7dac8c5ac9b26de27051881586caf5", "_created": "2026-05-29T07:48:44.000Z", "_published": "2026-05-29T09:03:29.317Z", "_jobs": [ { "job": 78460074289, "time": 195, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7285811781" }, { "job": 78460074305, "time": 285, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7285837605" }, { "job": 78460074324, "time": 366, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7285859758" }, { "job": 78460074308, "time": 168, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7287032090" }, { "job": 78460074327, "time": 202, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7287044854" }, { "job": 78459091988, "time": 431, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285755095" }, { "job": 78460074286, "time": 170, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285804501" }, { "job": 78460074322, "time": 252, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7285828640" }, { "job": 78460074311, "time": 257, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7285829838" }, { "job": 78460074314, "time": 239, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7285824362" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624858892", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/infinityFlow", "_commit": { "id": "aebfdae58d1a58c1bd01a700bd36b41c1bdd9780", "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": 1777380792 }, "_maintainer": { "name": "Etienne Becht", "email": "etienne.becht@protonmail.com" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "flowCore", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "pbapply", "role": "Imports" }, { "package": "matlab", "role": "Imports" }, { "package": "png", "role": "Imports" }, { "package": "raster", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "uwot", "role": "Imports" }, { "package": "gtools", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "generics", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "xgboost", "version": ">= 3.0.0", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "keras", "role": "Suggests" }, { "package": "tensorflow", "role": "Suggests" }, { "package": "glmnetUtils", "role": "Suggests" }, { "package": "e1071", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-51", "n": 4 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.23.0", "bioc": "3.24" }, { "branch": "release", "version": "1.22.0", "bioc": "3.23" } ], "_topics": [ "software", "flowcytometry", "cellbasedassays", "singlecell", "proteomics" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 372, "source": "https://www.bioconductor.org/packages/stats/bioc/infinityFlow" }, "_searchresults": 13, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/infinityFlow.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "fitter_glmnet", "fitter_linear", "fitter_nn", "fitter_svm", "fitter_xgboost", "infinity_flow", "select_backbone_and_exploratory_markers" ], "_datasets": [ { "name": "steady_state_lung", "title": "Subset of a massively parallel cytometry experiment of mouse lung single cells", "object": "steady_state_lung", "file": "steady_state_lung.rda", "class": [ "flowSet" ], "fields": [], "table": false, "tojson": false }, { "name": "steady_state_lung_annotation", "title": "Target and isotypes annotation for the data object infinityFlow::steady_state_lnug", "object": "steady_state_lung_annotation", "file": "steady_state_lung_annotation.rda", "class": [ "data.frame" ], "fields": [ "Infinity_target", "Infinity_isotype" ], "rows": 10, "table": true, "tojson": true }, { "name": "steady_state_lung_backbone_specification", "title": "Backbone and Infinity antibodies specification for the data object infinityFlow::steady_state_lnug", "object": "steady_state_lung_backbone_specification", "file": "steady_state_lung_backbone_specification.rda", "class": [ "data.frame" ], "fields": [ "name", "desc", "type" ], "rows": 22, "table": true, "tojson": true } ], "_help": [ { "page": "fitter_glmnet", "title": "Wrapper to glmnet. Defined separetely to avoid passing too many objects in parLapplyLB", "topics": [ "fitter_glmnet" ] }, { "page": "fitter_linear", "title": "Wrapper to linear model training. Defined separetely to avoid passing too many objects in parLapplyLB", "topics": [ "fitter_linear" ] }, { "page": "fitter_nn", "title": "Wrapper to Neural Network training. Defined separetely to avoid passing too many objects in parLapplyLB", "topics": [ "fitter_nn" ] }, { "page": "fitter_svm", "title": "Wrapper to SVM training. Defined separetely to avoid passing too many objects in parLapplyLB", "topics": [ "fitter_svm" ] }, { "page": "fitter_xgboost", "title": "Wrapper to XGBoost training. Defined separetely to avoid passing too many objects in parLapplyLB", "topics": [ "fitter_xgboost" ] }, { "page": "infinity_flow", "title": "Wrapper to the Infinity Flow pipeline", "topics": [ "infinity_flow" ] }, { "page": "select_backbone_and_exploratory_markers", "title": "For each parameter in the FCS files, interactively prompts whether it is part of the Backbone, the Infinity (exploratory) markers or should be ignored.", "topics": [ "select_backbone_and_exploratory_markers" ] }, { "page": "steady_state_lung", "title": "Subset of a massively parallel cytometry experiment of mouse lung single cells", "topics": [ "steady_state_lung" ] }, { "page": "steady_state_lung_annotation", "title": "Target and isotypes annotation for the data object infinityFlow::steady_state_lnug", "topics": [ "steady_state_lung_annotation" ] }, { "page": "steady_state_lung_backbone_specification", "title": "Backbone and Infinity antibodies specification for the data object infinityFlow::steady_state_lnug", "topics": [ "steady_state_lung_backbone_specification" ] } ], "_rundeps": [ "BH", "Biobase", "BiocGenerics", "biocmake", "cpp11", "cytolib", "data.table", "dir.expiry", "dqrng", "filelock", "flowCore", "FNN", "generics", "gtools", "irlba", "jsonlite", "lattice", "matlab", "Matrix", "matrixStats", "pbapply", "png", "raster", "Rcpp", "RcppAnnoy", "RcppEigen", "RcppProgress", "Rhdf5lib", "RProtoBufLib", "RSpectra", "S4Vectors", "sitmo", "sp", "terra", "uwot", "xgboost" ], "_vignettes": [ { "source": "basic_usage.Rmd", "filename": "basic_usage.html", "title": "Basic usage of the infinityFlow package", "author": "Etienne Becht", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Package installation", "Setting up your input data", "Specifying the Backbone and Infinity antibodies", "Running the Infinity Flow computational pipeline", "Description of the output", "Conclusion", "Information about the R session when this vignette was built" ], "created": "2020-06-19 03:03:47", "modified": "2021-10-10 17:58:47", "commits": 13 }, { "source": "training_non_default_regression_models.Rmd", "filename": "training_non_default_regression_models.html", "title": "Training non default regression models", "author": "Etienne Becht", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Loading the example data", "Note on package design", "The regression_functions argument", "The extra_args_regression_params argument", "Neural networks", "Conclusion", "Information about the R session when this vignette was built" ], "created": "2020-06-25 17:49:47", "modified": "2025-12-19 10:07:01", "commits": 7 } ], "_score": 3.7160033436347994, "_indexed": false, "_nocasepkg": "infinityflow", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/infinityFlow", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.22.0", "date": "2026-05-29T07:51:50.000Z", "distro": "noble", "commit": "aebfdae58d1a58c1bd01a700bd36b41c1bdd9780", "fileid": "553925f0338599163b83f5547e0d565b5d7cbda0dd0ecacc3e00f46ea87a2e4a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624858892" }, { "r": "4.6.0", "os": "linux", "version": "1.22.0", "date": "2026-05-29T07:53:14.000Z", "distro": "noble", "commit": "aebfdae58d1a58c1bd01a700bd36b41c1bdd9780", "fileid": "b03c00e19a9f9b41533ae60bcd4e965819128a6b6c46d0b25179fa37ba465048", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624858892" }, { "r": "4.5.3", "os": "mac", "version": "1.22.0", "date": "2026-05-29T09:01:04.000Z", "commit": "aebfdae58d1a58c1bd01a700bd36b41c1bdd9780", "fileid": "10b7fcdaba77a09ae976d492222f1c7ade20737ad74bc0f6617f2bb8bafab83d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624858892" }, { "r": "4.6.0", "os": "mac", "version": "1.22.0", "date": "2026-05-29T09:01:22.000Z", "commit": "aebfdae58d1a58c1bd01a700bd36b41c1bdd9780", "fileid": "814bd74072da4e02a36b936a113e9101ce8d43adc07dfcee30ca9c8f08894547", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624858892" }, { "r": "4.6.0", "os": "wasm", "version": "1.22.0", "date": "2026-05-29T07:52:06.000Z", "commit": "aebfdae58d1a58c1bd01a700bd36b41c1bdd9780", "fileid": "f069f56af2897c3ba1eef589b4e46c7b87b34c428e0a55f543dae2e7b188284f", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624858892" }, { "r": "4.7.0", "os": "win", "version": "1.22.0", "date": "2026-05-29T07:50:47.000Z", "commit": "aebfdae58d1a58c1bd01a700bd36b41c1bdd9780", "fileid": "eac406abcc856c50d86b8388b3daa304d5b6ca1be9ca286618de67428c232267", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624858892" }, { "r": "4.5.3", "os": "win", "version": "1.22.0", "date": "2026-05-29T07:50:53.000Z", "commit": "aebfdae58d1a58c1bd01a700bd36b41c1bdd9780", "fileid": "cda072bcf10d0ac302d37ec578e7416e39866f5a8081a6d168c254f4d88bd4f9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624858892" }, { "r": "4.6.0", "os": "win", "version": "1.22.0", "date": "2026-05-29T07:50:40.000Z", "commit": "aebfdae58d1a58c1bd01a700bd36b41c1bdd9780", "fileid": "b5ac18e0265d51063d8d3b0312a6d34aba643650de02610469b453f99755cb5c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624858892" } ] }