cellxgene

A React + Redux web application for exploring large scale single cell RNA sequence data.

Requirements

• OS: OSX, Windows, Linux
• python 3.6
• npm
• Google Chrome

Installation

clone project

git clone https://github.com/chanzuckerberg/cellxgene.git

install client

cd cellxgene
./bin/build-client

To use with virtual env for python (optional, but recommended)

ENV_NAME=cellxgene
python3 -m venv ${ENV_NAME}
source ${ENV_NAME}/bin/activate

install server

python3 setup.py install

commandline help

cellxgene --help
# For help with the scanpy engine
cellxgene scanpy --help

run (with demo data)

cellxgene --title PBMC3K scanpy example-dataset/

Thanks to Alex Wolf his help with test data