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Trevor notes:
> @mccalluc: it would be good to check the dtypes in `umap = ann_data.obsm['X_umap']`. I would be surprised if the hdf5 data used unnecessarily large dtypes, but pandas defaults to floa…
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@mruffalo : Looking back at this again, is it sufficiently precise to just look for the `.h5ad` extension, or is the same file format likely to be used for other kinds of data? If it's not sufficientl…
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> sceasy::convertFormat(h5ad_file, from="anndata", to="seurat", outFile='neurons.rds')
Loading required namespace: Seurat
/home/sherine/R/x86_64-pc-linux-gnu-library/4.3/reticulate/python/rpytools/l…
Flu09 updated
1 month ago
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I am trying to run chioso on an Ubuntu machine. What does the following error mean? Is it about h5ad formatting? (I converted from RDS to h5ad)
Could you share the desired format for gene list? I cur…
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Transferred issue from here:
https://github.com/rasmushenningsson/SingleCell10x.jl/issues/5
Hi Rasmus,
Just for fun, I thought I'd try applying `SingleCellProjections` to a dataset I had on…
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I am trying to read an h5ad file using
`df = vaex.open("../GSE99254_clusters_annotated.h5ad")`
However it fails with the following error
![image](https://user-images.githubusercontent.com/28567…
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sce
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Hi Sina,
Great work! Thanks for also hosting the code!
Would it be possible to have the `data.h5ad`? (I understand I can do this at my end, but will appreciate a more ready access)
Thanks,
S…
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Hi,
I have two .h5ad files from different datasets. Is there a way I can either (1) build a reference that combines these two (will I need to do integration etc.) or (2) during spot deconvolution i…
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Hi,
I am trying to run Cellphonedb v3 as below but encounter unexpected error. Do you know how to fix this error? Thanks!