Package: OSCA.advanced
Title: Advanced Single-Cell Analysis
Version: 1.21.2
Date: 2026-07-28
Authors@R: c( 
        person('Robert', 'Amezquita', role = 'aut'), 
        person('Aaron', 'Lun', role = 'aut'), 
        person('Stephanie', 'Hicks', role = 'aut'), 
        person('Raphael', 'Gottardo', role = 'aut'),
        person('Ludwig', 'Geistlinger', role = 'cre', email = "ludwig_geistlinger@hms.harvard.edu"),
        person('Peter', 'Hickey', role = 'ctb')
    )
Description: Deploys the advanced analysis chapters for the
        "Orchestrating Single Cell Analysis with Bioconductor" book.
        This describes the more complex steps of a single-cell RNA-seq
        analysis ranging from doublet detection, cell cycle assignment,
        specific steps for processing droplet data, nuclei-specific
        analyses, trajectory analyses, integrated analyses with protein
        abundances, and interactive visualization. It also elaborates
        on some of the basic analysis steps, focusing on alternative
        strategies and theoretical considerations. It is intended for
        readers who are already familiar with basic single-cell
        analyses, possibly after reading some of the prior books in
        this collection.
Depends: AnnotationHub, batchelor, BiocFileCache, BiocNeighbors,
        BiocParallel, BiocSingular, bluster, clustree, corral, densvis,
        DropletTestFiles, DropletUtils, edgeR, ggbeeswarm, ggplot2,
        gridExtra, igraph, iSEE, limma, msigdbr, mumosa, org.Mm.eg.db,
        pheatmap, rebook, rmarkdown, Rtsne, scater, scDblFinder, scPCA,
        scran, scrapper, scRNAseq (>= 2.17.9), scuttle, SingleR,
        slingshot, snifter, TENxBrainData, tradeSeq, TSCAN,
        velociraptor, viridis
Imports: OSCA.workflows, OSCA.basic, OSCA.multisample
Suggests: rmarkdown, knitr
VignetteBuilder: knitr
License: CC BY 4.0
URL: https://github.com/OSCA-source/OSCA.advanced
biocViews: ImmunoOncologyWorkflow, Workflow, SingleCellWorkflow
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libmagick++-dev gsfonts libbz2-dev libicu-dev
        liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev perl
        python3 libnode-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-28 09:26:32 UTC
RemoteUrl: https://github.com/bioc/OSCA.advanced
RemoteRef: HEAD
RemoteSha: 2f1050180630665e196962cde3c2742ddd066a51
NeedsCompilation: no
Packaged: 2026-10-10 10:56:27 UTC; root
Author: Robert Amezquita [aut],
  Aaron Lun [aut],
  Stephanie Hicks [aut],
  Raphael Gottardo [aut],
  Ludwig Geistlinger [cre],
  Peter Hickey [ctb]
Maintainer: Ludwig Geistlinger <ludwig_geistlinger@hms.harvard.edu>