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Hi!
I'm running your tool on a jupyter notebook (python 3.12, macos) using an anndata generated with scanpy (1.10.1)
I got this error message when running get_pseudobulk():
![image](https://gi…
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Hi Kai,
I have an anndata.AnnData, I can generate the snapatac2.AnnData as followed
```
# ann is an anndata.AnnData
sa2ann = snapatac2.AnnData(filename = "tmp.h5ad", X = ann.X)
```
When I perf…
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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…
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R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY…
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Anndata throws an error when trying to access for example `.obs`: `Error: Expected a python object, received a character`
Might be related to rstudio/reticulate#1531
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When we redesign the single-cell workbench page, I think it would be a great time to update the scanpy and anndata packages. I made a branch "scanpy-1.9.8-upgrade" where I will install the latest ver…
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I came across a previous issue #436 and couldn't get the dask solution working with my application, so I came up with a somewhat hacky solution to reading only the desired fields from an h5ad into an …
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**Description**
When an anndata object is deleted in the current scope the underlying memory is not (reliably) freed as it is for numpy and others. The memory is kept allocated until the process exi…
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Installed scTE in a Conda environment but kept getting problems until I upgraded to python 3.9
When python=3.6, I couldn't install a recent enough version of scipy (required scipy >= 1.8, but 1.8 dep…
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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…