fig:score-heatmap-grun
fig:score-heatmap-grun-donor
fig:score-dist-grun
fig:grun-beta-heat
fig:grun-beta-heat2
fig:grun-beta-heat-all
fig:grun-label-clusters
fig:heat-combined
fig:delta-combined
fig:pbmc-mono-heat
fig:heat-harmony
fig:unref-pancreas-score-heatmap
fig:unref-pancreas-delta-dist
fig:unref-pancreas-marker-heat
fig:unref-pancreas-label-clusters
fig:unref-pancreas-label-tsne
fig:unref-brain-score-heatmap
fig:unref-brain-delta-dist
fig:unref-brain-marker-heat
fig:unref-brain-label-clusters
fig:unref-brain-label-tsne
introduction
motivation
method-description
quick-start
where-to-get-help
classic-mode
overview
annotating-the-test-dataset
interaction-with-quality-control
choices-of-assay-data
reference-choice
sc-mode
overview-1
annotation-with-test-based-marker-detection
defining-custom-markers
pseudo-bulk-aggregation
annotation-diagnostics
overview-2
based-on-the-scores-within-cells
based-on-the-deltas-across-cells
based-on-marker-gene-expression
comparing-to-unsupervised-clustering
using-multiple-references
overview-3
using-reference-specific-labels
comparing-scores-across-references
combining-inferences-from-individual-references
combined-diagnostics
using-harmonized-labels
sharing-information-during-marker-detection
manual-label-harmonization
exploiting-the-cell-ontology
motivation-1
basic-manipulation
adjusting-resolution
advanced-options
preconstructed-indices
parallelization
approximate-algorithms
cluster-level-annotation
pancreas-case-study
loading-the-data
applying-the-annotation
diagnostics
comparison-to-clusters
cross-annotating-mouse-brains
loading-the-data-1
applying-the-annotation-1
diagnostics-1
comparison-to-clusters-1
contributors
bibliography