fig:sce-structure
fig:scworkflow
fig:quick-start-umap
fig:quick-start2-umap
installation
overview
installing-software
installing-packages
comments-on-bioconductor-versioning
finding-relevant-packages
staying-up-to-date
learning-r
links-to-r-tutorials
code-formatting
getting-help
beyond-the-basics
getting-scrna-seq-datasets
overview-1
some-comments-on-experimental-design
creating-a-count-matrix
reading-counts-into-r
from-tabular-formats
from-cellranger-output
from-hdf5-based-formats
the-singlecellexperiment-class
overview-2
installing-required-packages
storing-primary-experimental-data
filling-the-assays-slot
adding-more-assays
further-comments
handling-metadata
on-the-columns
on-the-rows
other-metadata
subsetting-and-combining
single-cell-specific-fields
background
dimensionality-reduction-results
alternative-experiments
size-factors
column-labels
conclusion
analysis-overview
outline
quick-start-simple
quick-start-multiple-batches