Annotate Cell Types Using SingleR — anno

Performs automated cell type annotation using the SingleR package. Uses a reference dataset (e.g., from celldex) to annotate cells based on gene expression profiles.

Usage

anno_SingleR(
  seurat_obj = NULL,
  ref_obj = NULL,
  seurat_colnm = NULL,
  ref_colnm = NULL,
  assay_nm = NULL,
  layer_nm = "data"
)

Arguments

seurat_obj: A Seurat object to annotate
ref_obj: Reference dataset (matrix or SummarizedExperiment) with cell type labels
seurat_colnm: Character, column name in Seurat metadata containing cluster IDs for aggregation
ref_colnm: Character, column name in reference object containing cell type labels
assay_nm: Character, assay to use (default: NULL)
layer_nm: Character, layer/slot to use (default: "data")

Value

A Seurat object with added 'anno_SingleR' column in metadata

Examples

if (FALSE) { # \dontrun{
# Annotate using built-in reference
library(SingleR)
ref <- HumanPrimaryCellAtlasData()

stRNA <- anno_SingleR(
  seurat_obj = stRNA,
  ref_obj = ref,
  seurat_colnm = "seurat_clusters",
  ref_colnm = "label.main"
)
} # }