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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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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…
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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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I am trying to work outside of python command line and more in interaction with AnnData / scanpy. I am tempted to fork this package and patch it to make it work with AnnData objects directly somehow. …
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Hi there,
When storing a matrix with row names and column names in the `uns` slot, these are removed. I assume that is to align with the python `numpy` implementation where these are not supported.…
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Hi Ye,
Nice work!
I got an error:
" /MNT/second_drive/user_data ygc/local/lib/python3.8 / site - packages/sklearn/utils/deprecation py: 86: FutureWarning: Function setup_anndata is deprecated; …
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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.
- [ ] (optio…
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Hi, thank you for the nice tool!
I'm trying to run my own visium data with standard Space Ranger output(filtered_feature_bc_matrix.h5 and spatial/tissue_positions_list.csv are provided), but got this…
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**Is your feature request related to a problem? Please describe.**
It is not currently straightforward to pass external dataloaders to train a model. In particular, loading `torch.Tensor` data and di…
j-bac updated
2 months ago