{ "_id": "6a1866dbacfb0bcc41dc0471", "Package": "OSCA.advanced", "Title": "Advanced Single-Cell Analysis", "Version": "1.21.0", "Date": "2025-11-19", "Authors@R": "c( \nperson('Robert', 'Amezquita', role = 'aut'),\nperson('Aaron', 'Lun', role = 'aut'),\nperson('Stephanie', 'Hicks', role = 'aut'),\nperson('Raphael', 'Gottardo', role = 'aut'),\nperson('Ludwig', 'Geistlinger', role = 'cre', email = \"ludwig_geistlinger@hms.harvard.edu\"),\nperson('Peter', 'Hickey', role = 'ctb')\n)", "Description": "Deploys the advanced analysis chapters for the\n\"Orchestrating Single Cell Analysis with Bioconductor\" book.\nThis describes the more complex steps of a single-cell RNA-seq\nanalysis ranging from doublet detection, cell cycle assignment,\nspecific steps for processing droplet data, nuclei-specific\nanalyses, trajectory analyses, integrated analyses with protein\nabundances, and interactive visualization. It also elaborates\non some of the basic analysis steps, focusing on alternative\nstrategies and theoretical considerations. It is intended for\nreaders who are already familiar with basic single-cell\nanalyses, possibly after reading some of the prior books in\nthis collection.", "VignetteBuilder": "knitr", "License": "CC BY 4.0", "URL": "https://github.com/OSCA-source/OSCA.advanced", "biocViews": "ImmunoOncologyWorkflow, Workflow, SingleCellWorkflow", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libglpk-dev libgmp3-dev make\nlibharfbuzz-dev libmagick++-dev gsfonts libbz2-dev libicu-dev\nlibjpeg-dev liblzma-dev libpng-dev libtiff-dev libuv1-dev\nlibwebp-dev libxml2-dev libssl-dev perl python3 libnode-dev\nxz-utils zlib1g-dev", "Repository": "https://tempbioc.r-universe.dev", "Date/Publication": "2026-04-28 12:53:44 UTC", "RemoteUrl": "https://github.com/bioc/OSCA.advanced", "RemoteRef": "HEAD", "RemoteSha": "84c44efb72cfed29ab9e66d68ae4ea0763c02910", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 15:08:17 UTC", "User": "root" }, "Author": "Robert Amezquita [aut],\nAaron Lun [aut],\nStephanie Hicks [aut],\nRaphael Gottardo [aut],\nLudwig Geistlinger [cre],\nPeter Hickey [ctb]", "Maintainer": "Ludwig Geistlinger ", "MD5sum": "efc9b8ecbb3fb2719edecb8d3a3a1504", "_user": "tempbioc", "_type": "src", "_file": "OSCA.advanced_1.21.0.tar.gz", "_fileid": "07f8f6fa4a5306715bda9a85b794abfe50d2129f53271a2d0edb9c700d8d7798", "_filesize": 188214, "_sha256": "07f8f6fa4a5306715bda9a85b794abfe50d2129f53271a2d0edb9c700d8d7798", "_created": "2026-05-28T15:08:17.000Z", "_published": "2026-05-28T16:01:31.496Z", "_jobs": [ { "job": 78322436626, "time": 544, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7269817162" }, { "job": 78322436647, "time": 917, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7269973064" }, { "job": 78322436775, "time": 655, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7269863581" }, { "job": 78322436797, "time": 405, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7270855519" }, { "job": 78322436703, "time": 389, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7270835857" }, { "job": 78314453212, "time": 2254, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7269586212" }, { "job": 78322436645, "time": 499, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7269798431" }, { "job": 78322436653, "time": 714, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7269889475" }, { "job": 78322436913, "time": 739, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7269899462" }, { "job": 78322436725, "time": 637, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7269856601" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 9 }, "_buildurl": "https://github.com/r-universe/tempbioc/actions/runs/26581193540", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/OSCA.advanced", "_commit": { "id": "84c44efb72cfed29ab9e66d68ae4ea0763c02910", "author": "lshep ", "committer": "lshep ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380824 }, "_maintainer": { "name": "Ludwig Geistlinger", "email": "ludwig_geistlinger@hms.harvard.edu", "login": "lgeistlinger", "description": "", "uuid": 11871050 }, "_distro": "noble", "_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": "clustree", "role": "Depends" }, { "package": "corral", "role": "Depends" }, { "package": "densvis", "role": "Depends" }, { "package": "DropletTestFiles", "role": "Depends" }, { "package": "DropletUtils", "role": "Depends" }, { "package": "edgeR", "role": "Depends" }, { "package": "ggbeeswarm", "role": "Depends" }, { "package": "ggplot2", "role": "Depends" }, { "package": "gridExtra", "role": "Depends" }, { "package": "igraph", "role": "Depends" }, { "package": "iSEE", "role": "Depends" }, { "package": "limma", "role": "Depends" }, { "package": "msigdbr", "role": "Depends" }, { "package": "mumosa", "role": "Depends" }, { "package": "org.Mm.eg.db", "role": "Depends" }, { "package": "pheatmap", "role": "Depends" }, { "package": "rebook", "role": "Depends" }, { "package": "rmarkdown", "role": "Depends" }, { "package": "Rtsne", "role": "Depends" }, { "package": "scater", "role": "Depends" }, { "package": "scDblFinder", "role": "Depends" }, { "package": "scPCA", "role": "Depends" }, { "package": "scran", "role": "Depends" }, { "package": "scrapper", "role": "Depends" }, { "package": "scRNAseq", "version": ">= 2.17.9", "role": "Depends" }, { "package": "scuttle", "role": "Depends" }, { "package": "SingleR", "role": "Depends" }, { "package": "slingshot", "role": "Depends" }, { "package": "snifter", "role": "Depends" }, { "package": "TENxBrainData", "role": "Depends" }, { "package": "tradeSeq", "role": "Depends" }, { "package": "TSCAN", "role": "Depends" }, { "package": "velociraptor", "role": "Depends" }, { "package": "viridis", "role": "Depends" }, { "package": "OSCA.workflows", "role": "Imports" }, { "package": "OSCA.basic", "role": "Imports" }, { "package": "OSCA.multisample", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-33", "n": 1 }, { "week": "2025-41", "n": 4 }, { "week": "2025-43", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2025-47", "n": 3 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_topics": [ "immunooncologyworkflow", "workflow", "singlecellworkflow" ], "_stars": 14, "_contributors": [ { "user": "ltla", "count": 43, "uuid": 8166669 }, { "user": "petehaitch", "count": 35, "uuid": 1049741 }, { "user": "hpages", "count": 14, "uuid": 8810451 }, { "user": "lgeistlinger", "count": 13, "uuid": 11871050 }, { "user": "alanocallaghan", "count": 8, "uuid": 10779688 }, { "user": "lshep", "count": 6, "uuid": 18724380 }, { "user": "nturaga", "count": 2, "uuid": 2746443 }, { "user": "plger", "count": 1, "uuid": 9786697 } ], "_userbio": { "uuid": 144379419, "type": "organization", "name": "tempbioc" }, "_devurl": "https://github.com/osca-source/osca.advanced", "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/OSCA.advanced.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [], "_help": [], "_readme": "https://github.com/bioc/OSCA.advanced/raw/HEAD/README.md", "_rundeps": [ "abind", "alabaster.base", "alabaster.matrix", "alabaster.ranges", "alabaster.sce", "alabaster.schemas", "alabaster.se", "annotate", "AnnotationDbi", "AnnotationFilter", "AnnotationHub", "apcluster", "askpass", "assertthat", "assorthead", "AUCell", "babelgene", "backports", "base64enc", "basilisk", "batchelor", "beachmat", "beeswarm", "benchmarkme", "benchmarkmeData", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "biocmake", "BiocManager", "BiocNeighbors", "BiocParallel", "BiocSingular", "BiocStyle", "BiocVersion", "Biostrings", "bit", "bit64", "bitops", "blob", "bluster", "bookdown", "bslib", "BumpyMatrix", "cachem", "Cairo", "caTools", "celldex", "checkmate", "cigarillo", "circlize", "cli", "clue", "cluster", "ClusterR", "clustree", "CodeDepends", "codetools", "colorspace", "colourpicker", "combinat", "commonmark", "ComplexHeatmap", "coop", "corral", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "DelayedMatrixStats", "dendextend", "densvis", "DEoptimR", "dichromat", "digest", "dir.expiry", "doParallel", "dplyr", "dqrng", "DropletTestFiles", "DropletUtils", "DT", "dynamicTreeCut", "edgeR", "elasticnet", "EnsDb.Hsapiens.v86", "ensembldb", "evaluate", "ExperimentHub", "farver", "fastICA", "fastmap", "filelock", "FNN", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "future", "future.apply", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "GetoptLong", "ggbeeswarm", "ggforce", "ggplot2", "ggraph", "ggrastr", "ggrepel", "ggthemes", "GlobalOptions", "globals", "glue", "gmp", "GO.db", "gplots", "graph", "graphlayouts", "gridExtra", "GSEABase", "gtable", "gtools", "gypsum", "h5mread", "HCAData", "HDF5Array", "here", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "httr2", "igraph", "IRanges", "irlba", "iSEE", "isoband", "iterators", "jquerylib", "jsonlite", "jsonvalidate", "KEGGREST", "kernlab", "KernSmooth", "knitr", "labeling", "lambda.r", "lars", "later", "lattice", "lazyeval", "lifecycle", "limma", "listenv", "listviewer", "locfit", "magick", "magrittr", "mapproj", "maps", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mbkmeans", "mclust", "memoise", "metapod", "mgcv", "mime", "miniUI", "mixtools", "MouseGastrulationData", "msigdbr", "MultiAssayExperiment", "mumosa", "nlme", "openssl", "org.Hs.eg.db", "org.Mm.eg.db", "origami", "OSCA.basic", "OSCA.multisample", "OSCA.workflows", "otel", "pals", "parallelly", "pbapply", "pheatmap", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "princurve", "promises", "ProtGenerics", "purrr", "R.methodsS3", "R.oo", "R.utils", "R6", "ragg", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppML", "RcppProgress", "RcppTOML", "RCurl", "Rdpack", "rebook", "reshape2", "ResidualMatrix", "restfulr", "reticulate", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "Rigraphlib", "rintrojs", "rjson", "rlang", "rmarkdown", "RMTstat", "robustbase", "rprojroot", "Rsamtools", "RSpectra", "RSQLite", "rsvd", "rtracklayer", "Rtsne", "S4Arrays", "S4Vectors", "S7", "sass", "ScaledMatrix", "scales", "scater", "scDblFinder", "scPCA", "scran", "scrapper", "scRNAseq", "scuttle", "segmented", "Seqinfo", "shape", "shiny", "shinyAce", "shinydashboard", "shinyjs", "shinyWidgets", "SingleCellExperiment", "SingleR", "sitmo", "slingshot", "snifter", "snow", "sourcetools", "SparseArray", "sparseMatrixStats", "sparsepca", "SpatialExperiment", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "systemfonts", "TENxBrainData", "TENxPBMCData", "textshaping", "tibble", "tidygraph", "tidyr", "tidyselect", "tinytex", "tradeSeq", "TrajectoryUtils", "transport", "TSCAN", "tweenr", "UCSC.utils", "utf8", "uwot", "V8", "vctrs", "velociraptor", "vipor", "viridis", "viridisLite", "withr", "xfun", "xgboost", "XML", "xtable", "XVector", "yaml", "zellkonverter" ], "_score": 4.468347330412158, "_indexed": false, "_nocasepkg": "osca.advanced", "_universes": [ "tempbioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-05-28T15:21:24.000Z", "distro": "noble", "commit": "84c44efb72cfed29ab9e66d68ae4ea0763c02910", "fileid": "fee6c92817c0ad231ed4524ab2ccfd43d9807bffbb5b31e82eaff81713d6ab02", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/tempbioc/actions/runs/26581193540" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-05-28T15:17:18.000Z", "distro": "noble", "commit": "84c44efb72cfed29ab9e66d68ae4ea0763c02910", "fileid": "8981a2988646317ffe8c55092dd59779565584fd00a4d0c1f68551309c195677", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/tempbioc/actions/runs/26581193540" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-05-28T15:58:30.000Z", "commit": "84c44efb72cfed29ab9e66d68ae4ea0763c02910", "fileid": "0d333c9480a071d3810ca5d935cc8ffa78d1c1d89286e06a9faab667c1237a49", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/tempbioc/actions/runs/26581193540" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-05-28T15:57:29.000Z", "commit": "84c44efb72cfed29ab9e66d68ae4ea0763c02910", "fileid": "0f1ccc1e50b919c7cfbc16d715f45dac607ea71d02373ebead85a51041a91c92", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/tempbioc/actions/runs/26581193540" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-05-28T15:17:43.000Z", "commit": "84c44efb72cfed29ab9e66d68ae4ea0763c02910", "fileid": "41f9bce842c7a0f23d4552b02bd726444545b02d1120a520ebcaf3d65d42eac3", "status": "success", "buildurl": "https://github.com/r-universe/tempbioc/actions/runs/26581193540" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-05-28T15:18:11.000Z", "commit": "84c44efb72cfed29ab9e66d68ae4ea0763c02910", "fileid": "8fc6051f3c3253860b98b4d8189c8851cbfa9ffd23c7e4c6a0e8073af9a5b715", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/tempbioc/actions/runs/26581193540" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-05-28T15:18:18.000Z", "commit": "84c44efb72cfed29ab9e66d68ae4ea0763c02910", "fileid": "feaa7620af447545f6d4e4ebd7e56f6e7a40c79af778c28a3a8480c81675c314", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/tempbioc/actions/runs/26581193540" }, { "r": "4.6.0", "os": "win", "version": "1.21.0", "date": "2026-05-28T15:17:06.000Z", "commit": "84c44efb72cfed29ab9e66d68ae4ea0763c02910", "fileid": "fdc4be514df7d474e70d529d043f90cb45abfa72f07dc8daff8fb2ccd5e4e04c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/tempbioc/actions/runs/26581193540" } ] }