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AnnData --> Seurat, particularly now there is Seurat v4 trajectory stuff/automated annotation stuff/Monocl can import Seurat objects... this is important!
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Is there a galaxy tool for AnnData --> mtx format? This is rather critical for moving from Galaxy-Scanpy --> Cytoscape....
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### Please make sure these conditions are met
- [X] I have checked that this issue has not already been reported.
- [X] I have confirmed this bug exists on the latest version of anndata.
- [X] (o…
jday1 updated
1 month ago
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## Description
due to the server network, I can not run
img = sq.datasets.visium_hne_image()
adata = sq.datasets.visium_hne_adata()
so I downloaded the visium_fluo.h5ad on another computer …
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Hello,
I was wondering if it makes sense to replace x_i vector of gene expression with some other lower dimension loadings (such as PCs) in the step of computing the similarity kernel K(x_i, x_j)?…
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When I use the convertFormat function to convert a Seurat object, I encountered the following error. How can I resolve it?
The version of Seurat is 5.0, and the current conda environment has a numpy…
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Hello-
We're publishing some data as MuData in the HuBMAP consortium, and we're also planning to use it to store descriptions and annotations of objects in segmentation masks.
These descriptions…
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The current build of `scanpy-scripts` has packaged `anndata==0.7.6`. This is causing issues in downstream Galaxy tools, since `ebi-gxa/anndata_ops` requires `scanpy-scripts` and gets this old `anndata…
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Some interop with ark-analysis would be nice for running analyses and comparing and benchmarking. Seems like they are starting with AnnData interoperability themselves, mostly for the downstream analy…
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Having built the vector indexes on Census embeddings (#694 chanzuckerberg/cellxgene-census#1113), develop the Python API inside `cellxgene_census.experimental` to input an AnnData and identify the mos…