Package: OSCA.basic
Title: Single-Cell Analysis Basics
Version: 1.20.0
Date: 2025-09-29
Authors@R: c( 
        person('Robert', 'Amezquita', role = 'aut'), 
        person('Aaron', 'Lun', role = 'aut', email="infinite.monkeys.with.keyboards@gmail.com"), 
        person('Stephanie', 'Hicks', role = 'aut'), 
        person('Raphael', 'Gottardo', role = 'aut'),
        person('Peter', 'Hickey', role = 'cre', email="peter.hickey@gmail.com")
    )
Description: 
    Deploys basic analysis chapters for the "Orchestrating Single Cell Analysis with Bioconductor" book.
    This describes the steps of a simple single-cell RNA-seq analysis, involving quality control,
    normalization, various forms of dimensionality reduction, clustering into subpopulations, 
    detection of marker genes, and annotation of cell types. It is intended for users who already
    have some familiarity with R and want to get hands-on with some basic single-cell analyses.
Depends: AnnotationHub, apcluster, AUCell, BiocFileCache, BiocSingular,
        bluster, celldex, cluster, dendextend, dynamicTreeCut, GO.db,
        gridExtra, GSEABase, igraph, limma, mbkmeans, org.Mm.eg.db,
        pheatmap, rebook, rmarkdown, RMTstat, robustbase, Rtsne,
        scater, scran, scrapper, scRNAseq, scuttle, SingleR, statmod,
        viridis
Imports: OSCA.workflows
Suggests: rmarkdown, knitr, OSCA.advanced
VignetteBuilder: knitr
License: CC BY 4.0
URL: https://github.com/OSCA-source/OSCA.basic
biocViews: ImmunoOncologyWorkflow, Workflow, SingleCellWorkflow
git_url: https://git.bioconductor.org/packages/OSCA.basic
git_branch: RELEASE_3_23
git_last_commit: 71cb54c
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-29
NeedsCompilation: no
Packaged: 2026-04-29 15:42:43 UTC; biocbuild
Author: Robert Amezquita [aut],
  Aaron Lun [aut],
  Stephanie Hicks [aut],
  Raphael Gottardo [aut],
  Peter Hickey [cre]
Maintainer: Peter Hickey <peter.hickey@gmail.com>
