1.7 KiB
cellxgene
cellxgene is an interactive data explorer for single-cell transcriptomics data designed to handle large datasets (1 million cells or more) and integrate with your favorite analysis tools
getting started
install the package
> pip install cellxgene
preprocess the data for use with cellxgene (optional)
> cellxgene --prepare dataset.h5ad -o processed.h5ad
launch the web app
> cellxgene --launch processed.h5ad
features
inspiration and collaboration
We've been heavily inspired by several other related single-cell visualization projects:
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
help and contact
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. As mentioned above, please submit any feature requests or bugs as Github issues. We'd love to hear from you!