Package: OSCA.advanced
Title: Advanced Single-Cell Analysis
Version: 1.14.0
Date: 2024-07-01
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,
        PCAtools, pheatmap, rebook, rmarkdown, Rtsne, scater,
        scDblFinder, scPCA, scran, 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
git_url: https://git.bioconductor.org/packages/OSCA.advanced
git_branch: RELEASE_3_20
git_last_commit: 16871ae
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2025-01-22
NeedsCompilation: no
Packaged: 2025-01-22 22:57:15 UTC; biocbuild
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>
