Exploratory CellxGene

Overview

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.

Installation

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

				
					cd
				
			

Activate the exCXG environment

				
					conda activate exCXG
				
			

Launch exCellxGene

				
					excellxgene launch curio.h5ad
				
			

Launch exCellxGene

Removing background

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Creating gene plots

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Subsetting data

				
					./
				
			

Merge and Analyze Multiple Datasets

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