This short introduction aims to show the installation and the setup process for CellxGene and Explore CellxGene.

It shows how to transform a Seurat object into an .h5ad file as well as the installation instructions for the 2 programs.

Using the SeuratDisk package in R.

library(Seurat)
library(SeuratDisk)

SaveH5Seurat(so, filename = "so.h5Seurat")
Convert("so.h5Seurat", dest = "h5ad")

The resulting .h5ad file is compatible with CellxGene and all of its extensions.

Installation instructions are from the CellxGene Website. Python 3.6+ is required and it is recommended to install to a conda/virtual environment.

pip intall cellxgene

launch from local file in current directory:

cellxgene launch example.h5ad --open

or from url:

cellxgene launch https://cellxgene-example-data.czi.technology/pbmc3k.h5ad

CELLxGENE Annotate currently supports the following browsers:

• Google Chrome 61+
• Edge 15+
• Firefox 60+

Installation instructions are from the exCellxGene GitHub. Python 3.9 is required and it is recommended to install to a conda/virtual environment.

conda create -n cxg python=3.9
conda activate cxg

Install excellxgene with pip:

pip install excellxgene

launch from local file in current directory:

excellxgene launch example.h5ad --open