cellxgene

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chore(deps): bump terser from 5.14.1 to 5.14.2 in /client

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Bumps [terser](https://github.com/terser/terser) from 5.14.1 to 5.14.2. Changelog Sourced from terser's changelog. v5.14.2 Security fix for RegExps that should not be evaluated (regexp DDOS) Source maps improvements (#1211) Performance improvements in...

dependabot[bot]

When specifying an S3 URL for `--user-generated-data-dir` option, cellxgene fails to launch with `Error: Unable to create directory specified by --user-generated-data-dir`. This feature was added by https://github.com/chanzuckerberg/cellxgene/pull/2512.

atolopko-czi

favicon not displaying

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As of d753441acccd66cfea50166b7a642ffab663d55a, favicon is failing to be displayed. This is causing `test_static` tests to fail in `test_api.py`. This diff looks implicated: `git diff de44739f8b11619e337e490942098f5c8d5f5b30 -- client/configuration/webpack/webpack.config.dev.js`: ``` diff --git...

atolopko-czi

[FEATURE REQUEST] Set custom default for expression clip range

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**Is your feature request related to a problem? Please describe.** Since many of the genes in our dataset have a few cells with high counts, we end up manually setting...

bnovotny

Better truncation on category labels

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We don't want to show 500,000 labels, if there is one label per cell, for instance (easy decision, performance, usability) Current method (naive):   The tool could be smarter...

colinmegill

feat: enable use of SOMA data format in desktop app with soma_adaptor

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#### Reviewers @Bento007 @ebezzi --- ## Changes - added `soma_adaptor.py`, extending `data_adaptor.py` similarly to `anndata_adaptor.py` - added unit tests plus related files, such as example/testing datasets and schema layout -...

roaga

[BUG] s3 .h5ad files larger than 1 GB don't launch

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**Describe the bug** Cellxgene fails to launch s3 datasets (..h5ad files) that are larger than 1 GB **To Reproduce** Steps to reproduce the behavior: I'm using cellxgene version 1.0.1. We...

brookmay

Log/Linear y-axis scale toggle for right sidebar gene expression

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After differential expression has been calculated, cellxgene displays histograms to visualize the distribution of a selected gene across all cells on the right sidebar. However, many genes are sparsely observed...

ambrosejcarr

[BUG] adding --backed does not reduce memory consumption for s3 files

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**Describe the bug** Cellxgene processes fail when I try to open resonably-sized files (~4GB) from s3. I've tried using --backed mode, but it did not reduce memory consumption. **Tested** Prepared...

arogozhnikov

Visium data visualization: enabling histology image to be overlaid and co-zoommed[FEATURE REQUEST]

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I have 10X Visium data for a spatial transcriptomics project. Although I'm able to use the spatial coordinates for the cellxgene embedding, I'm not able to put the image on...

brianpenghe