cellxgene

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Can Ergen states that the dot size scaling causes spots to become too large when zooming into embeddings that use (x, y) spatial coordinates, such as those discussed in #2056...

ambrosejcarr

[BUG] Gene sets file is ignored if it points to s3

4

**Describe the bug** ```bash # This works cellxgene launch s3:///test_data.h5ad --gene-sets-file /local/gene_sets.csv --port 5005 # This doesn't work cellxgene launch s3:///test_data.h5ad --gene-sets-file s3:///gene_sets.csv --port 5005 ``` First command shows gene...

arogozhnikov

Combining ExCellxgene with CellxGene VIP

2

In line with what the title asks - I've been using CellxGene VIP for downstream analysis, and recently found the newer ExCellxGene for preprocessing. Is it possible to combine these...

jackbrougher

support viz of >2D embeddings

9

if the selected embedding has >2 dimensions, expose the third dimension in some way brainstorm of ideas: - let user select which dimensions are plotted on which axes - full...

neuromusic

Fix desktop cellxgene ubuntu 3.9 build

1

The desktop cellxgene build for ubuntu 3.9 is [failing](https://github.com/chanzuckerberg/cellxgene/runs/4221930006?check_suite_focus=true). Looks like pip is trying to build from source and erroring with: ``` error in louvain setup command: use_2to3 is invalid...

atolopko-czi

Clarify installation recommendation with Conda

4

We currently recommend installation of cellxgene in conda using pip, which is brittle to scientists installing additional packages using `conda install`. Friederike Dundar suggests that we either maintain a conda...

ambrosejcarr

Clean up f/e code to be metadata schema agnostic (does not need to support corpora features)

1

Clean up f/e code to be metadata schema agnostic (does not need to support corpora features)

signechambers1

Consider removing custom make_var_unique code

1

There was a [bug](https://github.com/theislab/anndata/pull/345) in anndata that caused the `make_unique` function to not make var names unique. We created a [workaround](https://github.com/chanzuckerberg/cellxgene/blob/main/server/cli/prepare.py#L231) in `cellxgene prepare`. The bug in anndata has been...

mckinsel

Update d3 to v5, ensure using only specific modules

1

colinmegill

debt: update webpack config to use asset loader

1

Webpack will be deprecating url-loader, file-loader and raw-loader "soon". Need to update the build config to use asset loading. https://webpack.js.org/guides/asset-modules/

bkmartinjr