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Hi, I would like to ask, for the h5ad file input by cellbender, should I use the raw data or the filtered data?
Thank you for your time, thank you!
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Hey Kai,
Thanks so much for developing snapATAC2. I've been using it for a bit and really like it! I do have one question regarding working with files in backed mode. When we import fragment files …
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I noticed that the link to the data in .h5ad format in the code is no longer working. Do you still have these data saved? If so, could you please send me a copy? My email is [haoyu.wangg@gmail.com].Th…
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Thank you for this great tool.
I have finished integrating and annotating my data which could not have been done without this tool. Now I need to convert the object to h5ad to do some downstream anal…
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When click data file 'bpmc3k.h5ad', got server error "The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there is an error in the appl…
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## Motivation
- Make memory requirements predictable
- Reduce datasets processing failure due to OOM
## Definition of Done
- Validate and write datasets in constant memory
- eliminate the u…
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Hi,
Thank you for making all these scRNAseq analysis resources.
I have been trying to follow the given example [here](https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html) to …
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Is there a pre-trained cell type annotation model available with weights that can be directly used on the MS dataset?
elif DATASET == 'MS':
data_train = ad.read_h5ad(f'../data/c_data.h5ad')
…
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I got a 3D figure plotted by h5ad file, which is constructed by other software.
![image](https://github.com/user-attachments/assets/2223f925-7c80-47d9-af2a-b3bbbab2f941)
I want to known, Is …
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Hi, is it possible to run SEVtras part I with all the raw cellranger outputs for multiple samples already in an anndata or does it need to be run by providing the raw cellranger outputs separately?