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Hello,
I've been trying to deploy cellxgene-gateway using a python WSGI HTTP server like Gunicorn, since Flask only provides a dev server. I am also using nginx as a reverse proxy to forward client …
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[This PR](https://github.com/chanzuckerberg/single-cell-data-portal/pull/5705/files) added primary_cell_count to the dp and discover APIs, with the intent to have the FE consume the datasets/index end…
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I do realise that SCEasy Converter is now new so maybe that's still something in the development stage, but currently it is not possible to select any datasets from the history as the input - shown be…
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**Describe the bug**
On constrained cases where maybe the object store cache size is not big enough, you can see the job requesting objects actually proceeding when some of the objects are not pres…
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**Describe the bug**
`de.test.versus_rest()` returns the wrong comparison for GLM tests (I have tested it with `test=wald`).
This is due to the comparison being made on the wrong coefficient, *i.e…
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I'm working on an extension of the AnnData object called [TreeData](https://github.com/YosefLab/treedata) which adds two additional fields `obst` and `vart` for storing `nx.DiGraph` trees for the `obs…
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Hello, Developer,
I encountered an issue while trying to save my integrated data as an h5ad file. Interestingly, I can save it as an h5ms file without any problems. Could you please explain why thi…
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Dear authors,
Thank you for your help again. I have a question about your code and data. In lpy.py, I found this function:
_def createAnnData(folderlist, prefix, souporcell_folderlist = None, so…
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I am looking to fine-tune scGPT on your data and need to convert .parquet files into .h5ad format. I have read the .parquet file into a DataFrame and found that df.X contains the gene expression matri…
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When exploring various options of preprocessing data, I try to avoid having several copies of AnnData objects in memory if they're not sparse, so I save them to h5ad at key steps. Sometimes alas, afte…