Cell-type annotation
====================

Asc-Seurat provides **automated cell-type annotation** via `SingleR
<https://bioconductor.org/packages/release/bioc/html/SingleR.html>`_.
Use the **Cell-type Annotation** entry under *Tools* to run SingleR
against a ``celldex`` reference atlas and attach predicted cell-type
labels to the clustered object. The module works on objects produced
by the Single Sample or Integration tabs, or on processed Seurat RDS
files uploaded directly.

.. figure:: images/v3/v3_cell_annotation.png
   :alt: Cell-type Annotation tab (SingleR).
   :width: 100%
   :align: center

   Cell-type Annotation tab. Point it at a processed Seurat object
   (from the Single Sample or Integration tab, or uploaded as RDS),
   choose a ``celldex`` reference atlas, and pick main or fine labels.