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Replace all content with redirects to scrapbook chapters. #21

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28 changes: 0 additions & 28 deletions .github/workflows/rebuild.yaml
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47 changes: 6 additions & 41 deletions DESCRIPTION
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Expand Up @@ -10,48 +10,13 @@ Authors@R: c(
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,
Most of the content in this book has been migrated to scrapbook (https://bioconductor.org/books/release/scrapbook).
This book is only retained to provide redirections to the relevant scrapbook chapters.
Depends: scrapbook
Suggest:
knitr,
OSCA.advanced
rmarkdown,
BiocStyle
VignetteBuilder: knitr
License: CC BY 4.0
URL: https://github.com/OSCA-source/OSCA.basic
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16 changes: 0 additions & 16 deletions inst/book/_bookdown.yml
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19 changes: 0 additions & 19 deletions inst/book/_output.yml
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454 changes: 0 additions & 454 deletions inst/book/cell-annotation.Rmd
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9 changes: 9 additions & 0 deletions inst/book/cell-type-annotation.html
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@@ -0,0 +1,9 @@
<!DOCTYPE html>
<html>
<head>
<link rel="canonical" href="https://bioconductor.org/books/release/SingleRBook">
<meta name="robots" content="noindex">
<meta http-equiv="content-type" content="text/html; charset=utf-8"/>
<meta http-equiv="refresh" content="0; url=https://bioconductor.org/books/release/SingleRBook"/>
</head>
</html>
621 changes: 0 additions & 621 deletions inst/book/clustering.Rmd
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9 changes: 9 additions & 0 deletions inst/book/clustering.html
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@@ -0,0 +1,9 @@
<!DOCTYPE html>
<html>
<head>
<link rel="canonical" href="https://bioconductor.org/books/release/scrapbook/clustering.html">
<meta name="robots" content="noindex">
<meta http-equiv="content-type" content="text/html; charset=utf-8"/>
<meta http-equiv="refresh" content="0; url=https://bioconductor.org/books/release/scrapbook/clustering.html"/>
</head>
</html>
9 changes: 9 additions & 0 deletions inst/book/dimensionality-reduction.html
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@@ -0,0 +1,9 @@
<!DOCTYPE html>
<html>
<head>
<link rel="canonical" href="https://bioconductor.org/books/release/scrapbook/principal-components-analysis.html">
<meta name="robots" content="noindex">
<meta http-equiv="content-type" content="text/html; charset=utf-8"/>
<meta http-equiv="refresh" content="0; url=https://bioconductor.org/books/release/scrapbook/principal-components-analysis.html"/>
</head>
</html>
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