AnnotateCellsWithSingleR

This function annotates the cells in a Seurat object using the SingleR package
with reference data obtained from the Celldex package.

Reports markers list, differentially expressed genes, associated pathways, cell-type annotations, does batch correction and other related single cell analyses all wrapped within 'Seurat'.

Viswanadham Sridhara

scPipeline

A Wrapper for 'Seurat' and Related R Packages for End-to-End
Single Cell Analysis

AnnotateCellsWithSingleR function

<dl><dt>seurat_object</dt>
<dd>A Seurat object to be annotated.</dd>
<dt>reference_data</dt>
<dd>A reference dataset to use for annotation (e.g., HumanPrimaryCellAtlasData from Celldex).
If NULL, HumanPrimaryCellAtlasData is used by default.</dd>
<dt>assay</dt>
<dd>The assay in the Seurat object to use for annotation. Default is "RNA".</dd></dl>

Arguments

Annotate cells in a Seurat object using SingleR with Celldex — AnnotateCellsWithSingleR

<dl>

<dt>seurat_object</dt>
<dd>A Seurat object to be annotated.</dd>


<dt>reference_data</dt>
<dd>A reference dataset to use for annotation (e.g., HumanPrimaryCellAtlasData from Celldex).
If NULL, HumanPrimaryCellAtlasData is used by default.</dd>


<dt>assay</dt>
<dd>The assay in the Seurat object to use for annotation. Default is "RNA".</dd>

</dl>

AnnotateCellsWithSingleR: Annotate cells in a Seurat object using SingleR with Celldex

Description

Usage

Value

Arguments