cellxgene

An interactive explorer for single-cell transcriptomics data

Quick start
Installation
Gallery
Cellxgene data portal
Demo datasets
Preparing your data
Launching cellxgene
Hosting cellxgene
Annotating data
Methods
Troubleshooting
Roadmap
Contributing (ideas or code)
Contact & finding help
Code

Installing cellxgene

Cellxgene has two parts:

Requirements

You’ll need python 3.6+ and an up-to-date version of Google Chrome. The web UI is tested on OSX and Windows using Chrome, and the python CLI is tested on OSX and Ubuntu (via WSL/Windows). It should work on other platforms, but if you run into trouble let us know.

Python.org has help on installing a recent version of Python, including the pip package manager. Chrome is available at Google.com/chrome.

Basic install using pip

To install the cellxgene explorer alone, run:

pip install cellxgene

To install cellxgene and the optional cellxgene prepare, run:

pip install cellxgene[prepare]

Note: if the aforementioned optional prepare package installation fails, you can also install these packages directly:

pip install scanpy>=1.3.7 python-igraph louvain>=0.6

On various Linux platforms, you may also need to install build dependencies first:

sudo apt-get install build-essential python-dev
pip install scanpy>=1.3.7 python-igraph louvain>=0.6

If you already have cellxgene installed, you can update to the most recent version by running:

pip install cellxgene --upgrade

Using a conda environment

To install cellxgene alone, run:

conda create --yes -n cellxgene python=3.7
conda activate cellxgene
pip install cellxgene

To install cellxgene and the optional cellxgene prepare, run:

conda create --yes -n cellxgene python=3.7
conda activate cellxgene
pip install cellxgene[prepare]

Using a virtual environment

To install cellxgene alone, run:

ENV_NAME=cellxgene
python3.7 -m venv ${ENV_NAME}
source ${ENV_NAME}/bin/activate
pip install cellxgene

To install cellxgene and cellxgene prepare, run:

ENV_NAME=cellxgene
python3.7 -m venv ${ENV_NAME}
source ${ENV_NAME}/bin/activate
pip install cellxgene[prepare]

Using docker

Build the image

docker build . -t cellxgene

Run the container and mount data (change data location, --port and --host parameters as needed)

docker run -v "$PWD/example-dataset/:/data/" -p 5005:5005 cellxgene launch --host 0.0.0.0 data/pbmc3k.h5ad

You will need to use --host 0.0.0.0 to have the container listen to incoming requests from the browser