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