AzimuthAPI

Current version: 1.0.0 | GitHub

AzimuthAPI is an R package that provides an interface to the Pan-human Azimuth neural network, enabling users to run cell type annotation on single-cell and spatial transcriptomics data.

Two options for annotation are available:

• CloudAzimuth: computation occurs on the cloud; requires no additional setup.

• ANNotate: computation occurs entirely locally in R via reticulate; requires a conda environment with panhumanpy installed.

Installation

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes") 
}

# Install AzimuthAPI from GitHub
remotes::install_github("satijalab/AzimuthAPI")

Quickstart

library(AzimuthAPI)
library(Seurat)

# Load data
obj <- ...

# Normalize
obj <- NormalizeData(obj)

# Run annotation on the cloud
obj <- CloudAzimuth(obj)

# Get cell type annotations
cell_metadata <- obj@meta.data

# Extract embeddings
embeddings <- Embeddings(obj, reduction = "azimuth_embed")

# Generate UMAP
obj <- RunUMAP(obj, dims = 1:128, reduction = "azimuth_embed", reduction.name = "azimuth_umap")

Tutorial

For an introductory tutorial, please check out this vignette (download here).

The vignette covers both cloud-based and local annotation, including setup.