Getting started

Installation

Requires Python 3.11+.

Install from source with uv:

git clone https://github.com/aaronwolen/cellxgene-discover-cli.git
cd cellxgene-discover-cli
uv sync

Basic usage

The main entry point is cxg list, which fetches and filters all public datasets from CELLxGene Discover.

# List all datasets
cxg list

# Filter by organism and tissue
cxg list --organism "Homo sapiens" --tissue brain

Use --help on any command or subcommand to see available options:

cxg --help
cxg dataset --help
cxg dataset list --help

Verbose output

Use -v for info-level logging or -vv for debug-level output:

cxg -v list --organism "Homo sapiens"
cxg -vv dataset view DATASET_ID

Command overview

Command	Description
cxg list	List and filter datasets (alias for cxg dataset list)
cxg dataset view	View details for a single dataset
cxg dataset download	Download one or more datasets
cxg collection list	List public collections
cxg collection view	View collection details
cxg field list	List all filterable dataset fields
cxg field values	Enumerate values for a filterable field
cxg cache status	Check cache age and size
cxg cache clear	Delete cached data
cxg config list	View current config file
cxg config get	Read a config value
cxg config set	Set a config value
cxg config path	Print config file path
cxg --install-completion	Install shell completions