Cluster Annotation

How to annotate clusters.

Label transfer

A good starting point for cluster annotation is to transfer labels from an existing dataset or external reference. To do so, click the label transfer toggle and select a dataset to transfer labels from:

Label Transfer

Change cluster name

To manually change a cluster name toggle the rename cluster button:

Manual Annotation

Then type a new name for the cluster and click the rename cluster button:

Rename Cluster

Sorting marker genes

Selecting a cluster will sort marker genes for that cluster:

Sort Markers

To compare the selected cluster to one other cluster, click the toggle single group comparisons button and select a comparison:

Rename Cluster

Comparing two clusters is particularly useful for distinguishing closely related clusters and for confirming doublet clusters.

Exploring marker genes

Selecting a gene will plot its logcounts in cells and clusters:

Plot Feature

External gene data

Click the BioGPS toggle button to view the relative expression of the selected gene in the groups from the BioGPS dataset:

Plot Feature

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