Cellxgene

Desktop 1.0 Release Notes

- Updated links to documentation
- Fixed a [bug](https://app.zenhub.com/workspaces/single-cell-5e2a191dad828d52cc78b028/issues/chanzuckerberg/cellxgene/2454) with label interactions
- Assorted maintenance

New features
* Python 3.9 support
* The latest gene added appears at the top of the list of genes in Quick Gene Search
* Updated front end package dependencies
* Assorted maintenance

Bug fixes
* Fixed a [bug](https://app.zenhub.com/workspaces/single-cell-5e2a191dad828d52cc78b028/issues/chanzuckerberg/cellxgene/2414) when renaming gene sets

New features
- Introduced CLI parameter [--X-approximate-distribution](https://github.com/chanzuckerberg/cellxgene/issues/2282) for users to specify the distribution of their data, and override the default heuristic determination
- For categories with the number of labels over the number set by --max-category-items (default 1000), we now include a label that aggregates all labels over the limit instead of truncating the list of labels

Breaking changes
- Removed support for experimental features (--experimental-annotations-ontology, --experimental-annotations-ontology-obo and --experimental-enable-reembedding)

Bug fixes
- Fixed a [bug](https://github.com/chanzuckerberg/cellxgene/issues/2211) in differential expression calculation by changing the t-test calculation to consistently assume normally distributed data, and to log data when data is not normally distributed based on a heuristic
- Fixed a [bug](https://github.com/chanzuckerberg/cellxgene/issues/2225) in --max-category-items

This release contains a new major feature: gene sets! A gene set is a list of genes. You will now be able to visualize the mean expression of a gene set and create and edit gene sets from the UI. Check out our user guide under docs for more information and how to get started.

We’ve also improved differential expression functionality. Now when you run differential expression, 2 lists will be created: one list of 50 highly expressed genes in group 1 and one list of 50 highly expressed genes in group 2.

Please note we will be deprecating Safari support with this release. Please use Chrome, Edge, or Firefox for the best experience.

**Summary**: There were two packages that had major updates that caused incompatibility issues with cellxgene: `flatbuffers` and `Flask`. In this release, we have pinned both packages to be below the latest 2.0 versions to avoid these incompatibilities (issue 2197).

**Summary:** This release contains bug fixes for a few issues with mismatched colors between the left sidebar and the main canvas (issues 2007 and 2011), and improved error handling for —experimental-annotations-ontology (issue 2024).