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DESCRIPTION
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DESCRIPTION
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Package: OSCA.basic
Title: Single-Cell Analysis Basics
Version: 0.99.17
Date: 2021-05-16
Authors@R: c(
person('Robert', 'Amezquita', role = c('aut')),
person('Aaron', 'Lun', role = c('aut', 'cre'), email="[email protected]"),
person('Stephanie', 'Hicks', role = 'aut'),
person('Raphael', 'Gottardo', role = 'aut')
)
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,
org.Mm.eg.db,
pheatmap,
rebook,
rmarkdown,
RMTstat,
robustbase,
Rtsne,
scater,
scran,
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