Installation

Requirements

The Census API requires a Linux or MacOS system with:

  • Python 3.7 to Python 3.10. Or R, supported versions TBD.

  • Recommended: >16 GB of memory.

  • Recommended: >5 Mbps internet connection.

  • Recommended: for increased performance use the API through a AWS-EC2 instance from the region us-west-2. The Census data builds are hosted in a AWS-S3 bucket in that region.

Python

(Optional) In your working directory, make and activate a virtual environment or conda environment. For example:

python -m venv ./venv
source ./venv/bin/activate

Install the cellxgene-census package via pip:

pip install -U cellxgene-census

R

The R package will be soon deposited into R-Universe. In the meantime you can directly install from github using the devtools R package.

From an R session:

install.packages("devtools")
devtools::install_github("chanzuckerberg/cellxgene-census/api/r/cellxgene.census")