{ "_id": "6aca1dfffe5cc25786e84dac", "Package": "OSCA.workflows", "Title": "OSCA Workflows", "Version": "1.20.0", "Date": "2025-10-10", "Authors@R": "c( \nperson('Robert', 'Amezquita', role = 'aut'),\nperson('Aaron', 'Lun', role = 'aut', email=\"infinite.monkeys.with.keyboards@gmail.com\"),\nperson('Stephanie', 'Hicks', role = 'aut'),\nperson('Raphael', 'Gottardo', role = 'aut'),\nperson('Peter', 'Hickey', role = 'cre', email=\"peter.hickey@gmail.com\")\n)", "Description": "Deploys the workflows of the \"Orchestrating Single Cell\nAnalysis with Bioconductor\" book. This contains worked case\nstudies of analyses of a variety of single-cell datasets, each\nproceeding from a SingleCellExperiment object. Exposition is\ngenerally minimal other than for dataset-specific\njustifications for parameter tweaks; refer to the other books\nin the OCSA collection for a detailed explanation of the\ntheoretical basis of each step. It is intended for readers who\nalready know the background and just want some code to copy and\npaste into their own analyses.", "VignetteBuilder": "knitr", "License": "CC BY 4.0", "URL": "https://github.com/OSCA-source/OSCA.workflows", "biocViews": "ImmunoOncologyWorkflow, Workflow, SingleCellWorkflow", "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nlibnode-dev xz-utils zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:53:42 UTC", "RemoteUrl": "https://github.com/bioc/OSCA.workflows", "RemoteRef": "RELEASE_3_23", "RemoteSha": "89b8665b7aa53f1750abec8e96e66ad538a06406", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-10 11:04:16 UTC", "User": "root" }, "Author": "Robert Amezquita [aut],\nAaron Lun [aut],\nStephanie Hicks [aut],\nRaphael Gottardo [aut],\nPeter Hickey [cre]", "Maintainer": "Peter Hickey ", "_user": "bioc-release", "_type": "src", "_file": "OSCA.workflows_1.20.0.tar.gz", "_fileid": "https://r2.ropensci.org/1adb616e8589f3843d1698f4ab0d3813ef10f24a99fc3db45c6d89f639b5d78c", "_filesize": 106930, "_sha256": "1adb616e8589f3843d1698f4ab0d3813ef10f24a99fc3db45c6d89f639b5d78c", "_expires": "2027-01-18T11:13:58.000Z", "_created": "2026-10-10T11:04:16.000Z", "_published": "2026-10-10T11:14:07.135Z", "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38046550438", "_status": "failure", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 9 }, "_upstream": "https://github.com/bioc/OSCA.workflows", "_commit": { "id": "89b8665b7aa53f1750abec8e96e66ad538a06406", "author": "lshep ", "committer": "lshep ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380822 }, "_maintainer": { "name": "Peter Hickey", "email": "peter.hickey@gmail.com", "login": "petehaitch", "description": "", "uuid": 1049741 }, "_distro": "resolute", "_jobs": [ { "job": 114198926075, "time": 243, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11668421343" }, { "job": 114198926079, "time": 422, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11668341630" }, { "job": 114198926080, "time": 498, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11668525781" }, { "job": 114197183317, "time": 622, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "11668006313" } ], "_registered": true, "_dependencies": [ { "package": "AnnotationHub", "role": "Depends" }, { "package": "batchelor", "role": "Depends" }, { "package": "BiocFileCache", "role": "Depends" }, { "package": "BiocNeighbors", "role": "Depends" }, { "package": "BiocParallel", "role": "Depends" }, { "package": "BiocSingular", "role": "Depends" }, { "package": "bluster", "role": "Depends" }, { "package": "celldex", "role": "Depends" }, { "package": "cluster", "role": "Depends" }, { "package": "DropletTestFiles", "role": "Depends" }, { "package": "DropletUtils", "role": "Depends" }, { "package": "dynamicTreeCut", "role": "Depends" }, { "package": "edgeR", "role": "Depends" }, { "package": "EnsDb.Hsapiens.v86", "role": "Depends" }, { "package": "gridExtra", "role": "Depends" }, { "package": "HCAData", "role": "Depends" }, { "package": "igraph", "role": "Depends" }, { "package": "limma", "role": "Depends" }, { "package": "org.Hs.eg.db", "role": "Depends" }, { "package": "org.Mm.eg.db", "role": "Depends" }, { "package": "pheatmap", "role": "Depends" }, { "package": "rebook", "role": "Depends" }, { "package": "rmarkdown", "role": "Depends" }, { "package": "scater", "role": "Depends" }, { "package": "scPCA", "role": "Depends" }, { "package": "scran", "role": "Depends" }, { "package": "scRNAseq", "role": "Depends" }, { "package": "scuttle", "role": "Depends" }, { "package": "SingleR", "role": "Depends" }, { "package": "viridis", "role": "Depends" }, { "package": "BiocManager", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2025-41", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24", "repository": "books" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23", "repository": "books" } ], "_topics": [ "immunooncologyworkflow", "workflow", "singlecellworkflow", "datapkg" ], "_stars": 4, "_contributors": [ { "user": "petehaitch", "count": 24, "uuid": 1049741 }, { "user": "hpages", "count": 13, "uuid": 8810451 }, { "user": "ltla", "count": 13, "uuid": 8166669 }, { "user": "alanocallaghan", "count": 4, "uuid": 10779688 }, { "user": "lshep", "count": 4, "uuid": 18724380 }, { "user": "nturaga", "count": 2, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/osca-source/osca.workflows", "_searchresults": 0, "_datapkg": true, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/OSCA.workflows.html", "extra/readme.html", "extra/readme.md" ], "_cranurl": false, "_exports": [], "_help": [], "_readme": "https://github.com/bioc/OSCA.workflows/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "alabaster.base", "alabaster.matrix", "alabaster.ranges", "alabaster.sce", "alabaster.schemas", "alabaster.se", "AnnotationDbi", "AnnotationFilter", "AnnotationHub", "askpass", "assertthat", "assorthead", "base64enc", "batchelor", "beachmat", "beeswarm", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "biocmake", "BiocManager", "BiocNeighbors", "BiocParallel", "BiocSingular", "BiocStyle", "BiocVersion", "Biostrings", "bit", "bit64", "bitops", "blob", "bluster", "bookdown", "bslib", "cachem", "celldex", "cigarillo", "cli", "cluster", "CodeDepends", "codetools", "coop", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "DelayedMatrixStats", "digest", "dir.expiry", "dplyr", "dqrng", "DropletTestFiles", "DropletUtils", "dynamicTreeCut", "edgeR", "elasticnet", "EnsDb.Hsapiens.v86", "ensembldb", "evaluate", "ExperimentHub", "farver", "fastmap", "filelock", "FNN", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "future", "future.apply", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggbeeswarm", "ggplot2", "ggrepel", "globals", "glue", "graph", "gridExtra", "gtable", "gypsum", "h5mread", "HCAData", "HDF5Array", "highr", "htmltools", "httr", "httr2", "igraph", "IRanges", "irlba", "isoband", "jquerylib", "jsonlite", "jsonvalidate", "KEGGREST", "kernlab", "knitr", "labeling", "lambda.r", "lars", "lattice", "lazyeval", "lifecycle", "limma", "listenv", "locfit", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "metapod", "mime", "openssl", "org.Hs.eg.db", "org.Mm.eg.db", "origami", "parallelly", "pheatmap", "pillar", "pkgconfig", "png", "ProtGenerics", "purrr", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppEigen", "RcppML", "RcppProgress", "RCurl", "Rdpack", "rebook", "ResidualMatrix", "restfulr", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "rjson", "rlang", "rmarkdown", "Rsamtools", "RSpectra", "RSQLite", "rsvd", "rtracklayer", "Rtsne", "S4Arrays", "S4Vectors", "S7", "sass", "ScaledMatrix", "scales", "scater", "scPCA", "scran", "scRNAseq", "scuttle", "Seqinfo", "SingleCellExperiment", "SingleR", "sitmo", "snow", "SparseArray", "sparseMatrixStats", "sparsepca", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "UCSC.utils", "utf8", "uwot", "V8", "vctrs", "vipor", "viridis", "viridisLite", "withr", "xfun", "XML", "XVector", "yaml" ], "_score": 4.954242509439325, "_indexed": false, "_nocasepkg": "osca.workflows", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/OSCA.workflows", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.20.0", "date": "2026-10-10T11:10:31.000Z", "distro": "resolute", "commit": "89b8665b7aa53f1750abec8e96e66ad538a06406", "fileid": "https://r2.ropensci.org/c1183789a74f0435e030b73241ddc468be1d55665c7f5af57ebe19e59b77df5f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38046550438" }, { "r": "4.6.1", "os": "linux", "version": "1.20.0", "date": "2026-10-10T11:11:17.000Z", "distro": "resolute", "commit": "89b8665b7aa53f1750abec8e96e66ad538a06406", "fileid": "https://r2.ropensci.org/ccb1fb771753846b0dfeedb41720469a8a24b523977029624163919ffe4e431d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/38046550438" } ] }