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support reading directly from Zarr-backed anndata files #713

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ngehlenborg opened this issue Aug 4, 2020 · 2 comments
Closed

support reading directly from Zarr-backed anndata files #713

ngehlenborg opened this issue Aug 4, 2020 · 2 comments
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feature New feature or request

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@ngehlenborg
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User story
anndata (https://anndata.readthedocs.io/en/latest/index.html) is a popular format for single cell data and supported by many tools. Vitessce should support native support for anndata files that are Zarr-backed.

Preferred solution
Implement parser for Zarr-backed anndata files to read expression data, observation, feature, and unstructured annotations.

image

(source: https://falexwolf.de/img/scanpy/anndata.svg)
@ngehlenborg ngehlenborg added the feature New feature or request label Aug 4, 2020
@ngehlenborg ngehlenborg mentioned this issue Aug 4, 2020
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@keller-mark
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keller-mark commented Aug 14, 2020 •
edited

Putting this conversion package here for future reference https://github.com/cellgeni/sceasy

and this https://github.com/theislab/anndata2ri

and this https://github.com/theislab/zellkonverter

@ilan-gold ilan-gold mentioned this issue Dec 8, 2020
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@keller-mark
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Closing because #807 was merged 😀

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@ngehlenborg @keller-mark