seurath5ad

This package extends Seurat to enable the loading of raw H5AD files generated by other platforms or tools. Only the obs and spatial information from the H5AD files will be imported.

Usage

library(seurath5ad)

#Example usage  
#Load a raw H5AD file  
seurat_object <- LoadRawH5ad("path/to/your/file.h5ad")

Installation

You can install the development version of seurath5ad from GitHub with:

# install.packages("devtools")
devtools::install_github("yiji-stomics/seurath5ad")

Note

When loading certain H5AD files, error messages may indicate that Seurat requires matrices in “double” format. It is essential to first convert the matrices to double format using Python.

import numpy as np
data.X = data.X.astype(np.double)