celltype_annotation

## SingleR (R)

library(Seurat)
library(SingleR)
library(celldex)
library(SummarizedExperiment)


ref <- celldex::HumanPrimaryCellAtlasData()
data <- readRDS("object.rds")
seurat_obj <- UpdateSeuratObject(object = data)
seurat_obj <- NormalizeData(seurat_obj)
seurat_obj <- ScaleData(seurat_obj)
results <- SingleR(test = as.SingleCellExperiment(seurat_obj), ref = ref, labels = ref$label.main)

# Add annotations to the object
seurat_obj$singlr_labels <- results$labels
--------------------------------------------------------------------------
## CellTypist (python)

import os
import scanpy as sc
import pandas as pd
import celltypist
from celltypist import models

adata = sc.read('object.h5ad')
model = models.Model.load(model = 'Immune_All_Low.pkl')
predictions = celltypist.annotate(adata, model = 'Immune_All_Low.pkl', majority_voting = True)
predictions.predicted_labels

# Add annotations to the object
adata = predictions.to_adata()