Web application for exploration of large scale scRNA-seq datasets
Project description
an interactive explorer for single-cell transcriptomics data
cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the Human Cell Atlas. Leveraging modern web development techniques to enable fast visualizations of at least 1 million cells, we hope to enable biologists and computational researchers to explore their data.
- Want to install and use cellxgene? Visit the cellxgene docs.
- Want to see where we are going? Check out our roadmap.
- Want to contribute? See our contributors guide.
quick start
To install cellxgene you need Python 3.6+. We recommend installing cellxgene into a conda or virtual environment.
Install the package.
pip install cellxgene
Download an example anndata file
curl -O https://cellxgene-example-data.czi.technology/pbmc3k.h5ad.zip
unzip pbmc3k.h5ad
Launch cellxgene
cellxgene launch pbmc3k.h5ad --open
To learn more about what you can do with cellxgene, see the Getting Started guide.
get in touch
Have questions, suggestions, or comments? You can come hang out with us by joining the CZI Science Slack and posting in the #cellxgene-users channel. Have feature requests or bugs? Please submit these as Github issues. We'd love to hear from you!
contributing
We warmly welcome contributions from the community! Please see our contributing guide and don't hesitate to open an issue or send a pull request to improve cellxgene.
This project adheres to the Contributor Covenant code of conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to opensource@chanzuckerberg.com.
core team
The current core team:
- Colin Megill, frontend & product design
- Bruce Martin, software engineer
- Sidney Bell, computational biologist
- Lia Prins, designer
- Severiano Badajoz, software engineer
We would also like to gratefully acknowledge contributions from past core team members:
- Charlotte Weaver, software engineer
where we are going
Our goal is to enable teams of computational and experimental biologists to collaboratively gain insight into their single-cell RNA-seq data.
There are 4 key features we plan to implement in the near term.
- Click install and launch
- Manual annotation workflows
- Toggle embeddings
- Gene information
For more detail on these features and where we are going, see our roadmap.
inspiration
We've been heavily inspired by several other related single-cell visualization projects, including the UCSC Cell Browswer, Cytoscape, Xena, ASAP, Gene Pattern, and many others. We hope to explore collaborations where useful as this community works together on improving interactive visualization for single-cell data.
We were inspired by Mike Bostock and the crossfilter team for the design of our filtering implementation.
We have been working closely with the scanpy team to integrate with their awesome analysis tools. Special thanks to Alex Wolf, Fabian Theis, and the rest of the team for their help during development and for providing an example dataset.
We are eager to explore integrations with other computational backends such as Seurat or Bioconductor
reuse
This project was started with the sole goal of empowering the scientific community to explore and understand their data. As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from this project, and reach out to us with ideas or questions. All code is freely available for reuse under the MIT license.
security
If you believe you have found a security issue, we would appreciate notification. Please send email to security@chanzuckerberg.com.
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