Exploratory CellxGene


Exploratory CellxGene (exCellxGene) is a tool for interactively exploring your Seeker data. 

exCellbyGene is developed and maintained by developers at the Chan Zuckerberg Biohub Network – San Francisco.


Follow the instructions below to install exCellxGene on your laptop or workstation.

1. Install Miniconda

2. Install exCellxGene

Create a new conda environment with Python 3.10

					conda create -n exCXG python=3.10 -y         

Activate the exCXG environment

					conda activate exCXG

Install exCellxGene and other necessary packages

					conda install -c conda-forge hdf5
pip3 install excellxgene==2.9.6
pip3 install -U pyopenssl

Firing up an instance of exCellxGene

Go to the folder containing your seeker data in h5ad format


Activate the exCXG environment

					conda activate exCXG

Launch exCellxGene

					excellxgene launch curio.h5ad

Launch exCellxGene

Removing background

<Scribe page>

Creating gene plots

<Scribe page>

Subsetting data


Merge and Analyze Multiple Datasets

<python script>

Table of Contents