Cellxgene Desktop Explorer is a tool in the cellxgene suite that enables collaborative exploratory analysis of single cell data and private data sharing.
This page describes how to quickly get started with exploratory analysis on your local computer. Those interested in hosting cellxgene to enable your collaborators to explore data from their browser without needing to download the data file or install cellxgene should see Self-Host Cellxgene.
To install cellxgene you need Python 3.6+. We recommend installing cellxgene into a conda or virtual environment.
Install the package, then launch cellxgene with an example AnnData file:
pip3 install cellxgene
cellxgene launch https://cellxgene-example-data.czi.technology/pbmc3k.h5ad
The following datasets are available on the web and can be opened directly using cellxgene launch
| Source | Cells | File Size | Raw Data | Processing |
|---|---|---|---|---|
| 10X genomics | 2638 | 19MB | Link | Notebook |
cellxgene launch https://cellxgene-example-data.czi.technology/pbmc3k.h5ad
| Source | Cells | File Size | Raw Data | Processing |
|---|---|---|---|---|
| bioRxiv, CZBiohub | 45423 | 174MB | Link | Notebook |
cellxgene launch https://cellxgene-example-data.czi.technology/tabula-muris.h5ad
| Source | Cells | File Size | Raw Data | Processing |
|---|---|---|---|---|
| bioRxiv, CZBiohub | 81478 | 3.9GB | Link | Notebook |
cellxgene launch https://cellxgene-example-data.czi.technology/tabula-muris-senis.h5ad