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I try to load a h5ad saved after cell2location without other operations.
visx=schard::h5ad2seurat_spatial('cell2location.spatial.scRNA.h5ad')
Error:
The h5ad seems to contain multiple visium sample…
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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! I am doing label transfer from reference dataset and classifying two query sets that should contain exactly same cell types. I noticed that running across several iterations the classifications wo…
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Hello,
1) I'd like to have a little more clarity on the QCs and parameters used to generate the cellbin UMAP on the SAW report.
I know stereopy is used, but I would like to know the values of th…
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Hi,
I am processing data generated with Smartseq2. For some reason, I merged all cells into one sorted and indexed BAM file, with each cell distinguished by the RG tag. I used the following command…
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Hello,
I am currently following a celltypist tutorial in which it can be used on a .h5ad object. My original object is Seurat, so I converted it first to h5Seurat and then to h5ad. I loaded in the…
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When using the stDiff-sc/dataset1_seq_1670.h5ad and stDiff-sp/dataset1_spatial_246_preprocess.h5ad datasets downloaded from Zenodo for training, I encountered the following error:
```bash
ValueErr…
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Hi I have an error when writing to an `h5ad` file using `write_h5ad` :
```
Error in py_call_impl(callable, dots$args, dots$keywords) :
TypeError: Can't implicitly convert non-string objects to…
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**Describe the bug**
*When trying to convert an h5ad file to zarr format using scarf I find that categorical keys are ignored.*
**To Reproduce**
```
>>> reader = scarf.H5adReader("/media/rpa…
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Hi TREASMO team,
paper looked really cool! So I wanted to try and run on some of my own data and the code provided:
rna = ad.read_h5ad('data/HSPC_Muon_RNA.h5ad')
atac = ad.read_h5ad('data/HSPC_Muon…