fig:qc-dist-416b
fig:qc-mito-zeisel
fig:qc-mito-spike-zeisel
fig:histlib
fig:deconv-zeisel
fig:norm-spike-t
fig:norm-effect-malat
fig:trend-plot-pbmc
fig:spike-416b
fig:tech-pbmc
fig:blocked-fit
fig:zeisel-scree
fig:zeisel-pca
fig:zeisel-pca-multi
fig:tsne-brain
fig:tsne-perplexity
fig:umap-brain
fig:tsne-clust-graph
fig:pbmc-force
fig:walktrap-v-others
fig:tsne-clust-kmeans
fig:tsne-clust-kmeans-best
fig:tsne-kmeans-graph-pbmc
fig:dend-416b
fig:dend-cluster
fig:tsne-416b
fig:tsne-kmeans-hclust-pbmc
fig:dendroid-pbmc
fig:tsne-kmeans-affinity-pbmc
fig:ccr7-dist-memory
fig:cd48-memory-expression
fig:pbmc-scored-markers-1
fig:pbmc-scored-markers-again
fig:pbmc-grouped-ranked-heat
fig:pbmc-grouped-ranked-heat2
fig:pbmc-markers-5-lfc
fig:blocked-markers-416b
fig:singler-heat-pbmc
fig:singler-cluster
fig:singler-comp-pancreas
fig:auc-dist
fig:aucell-muraro-heat
fig:violin-milk
fig:lipid-synth-violin
fig:thrsp-violin
quality-control
quality-control-motivation
common-choices-of-qc-metrics
identifying-low-quality-cells
fixed-qc
quality-control-outlier
other-approaches
quality-control-plots
quality-control-discarded
normalization
motivation
library-size-normalization
normalization-by-deconvolution
spike-norm
normalization-transformation
feature-selection
motivation-1
quantifying-per-gene-variation
sec:spikeins
variance-batch
hvg-selection
feature-selection-subsetting
dimensionality-reduction
overview
principal-components-analysis
choosing-the-number-of-pcs
visualizing-the-pcs
non-linear-methods-for-visualization
t-stochastic-neighbor-embedding
uniform-manifold-approximation-and-projection
visualization-interpretation
clustering
overview-1
clustering-graph
background
implementation
adjusting-the-parameters
vector-quantization-with-k-means
background-1
implementation-1
in-two-step-procedures
hierarchical-clustering
background-2
implementation-2
in-two-step-procedures-again
subclustering
marker-detection
motivation-2
scoring-markers-by-pairwise-comparisons
effect-sizes-for-pairwise-comparisons
summarizing-pairwise-effects
obtaining-the-full-effects
using-a-log-fold-change-threshold
marker-batch
cell-type-annotation
motivation-3
assigning-cell-labels-from-reference-data
overview-2
using-existing-references
using-custom-references
assigning-cell-labels-from-gene-sets
assigning-cluster-labels-from-markers
computing-gene-set-activities