cellxgene
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chanzuckerberg
An interactive explorer for single-cell transcriptomics data
There is a need to periodically validate that all Python requirements for the "desktop" (backend/server) variant exclude upstream deps with known vulnerabilities. Where they exist, minimum reuqired version for the...
From [Slack](https://czi-sci.slack.com/archives/CHTMHFU3A/p1635575670002900): Alexander Tarashansky: In backend/common/compute/diffexp_generic.py, (lines 122-133): ``` with np.errstate(divide="call", invalid="call", call=fp_err_set): n = X.shape[0] if sparse.issparse(X): mean = X.mean(axis=0).A1 dfm = X - mean # This is going...
After installing Python via Anaconda, I'm trying to download the course config file as instructed in https://chanzuckerberg.github.io/scRNA-python-workshop/intro/setup.html . However, when I click to download I'm brought to a Google Drive...
Hi, the new gene set tools are very valuable. However, a critical missing piece is allowing users to supply pre-specified labeled lists of genes (to avoid creating such lists with...
The cellxgene desktop GHA compatibility matrix tests have intermittently failing jobs, all failing at the `smoke-test-annotations` step. E.g. see https://github.com/chanzuckerberg/cellxgene/actions/runs/1243692946. May be timing-related.
As an eBio, I want to know what cells I have selected as I collapse and uncollapse genes within a gene set and collapse gene sets. Right now, it's very...
**Is your feature request related to a problem? Please describe.** It's currently difficult to run the cellxgene server behind a reverse proxy at a path other than `/` because no...
Our reducer/redux files do not maintain the same casing style across their filenames, exports, and imports. They must be refactored to follow the same standard across all uses. Taken from...
**The performance issue** On the Azimuth dataset, which has approximately 1 million cells and 77,000 genes, it takes ~4-5 seconds for colorby of an unloaded gene set to occur after...
**The performance issue** On the Azimuth dataset, which has approximately 1 million cells and 77,000 genes, a gene set of 194 genes takes 105s to fully load. **To Reproduce** Steps...
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An interactive explorer for single-cell transcriptomics data