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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 scanpy.
- [ ] (op…
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Hello,
In my opinion, all dependencies are very common and/or lightweight, except `datashader` which requires `dask`/`xarray`/`pillow` among others. Since it is used in only one plot function, shou…
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### Description of feature
Hi, this tool looks like a great way to perform pseudo-bulk DEA. May I asked how is the development progress and whether it is ready to be used!
Thanks!
SNOL2 updated
7 months ago
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@lillux In DBiT seq reader there's a step in which spots are sorted in place by their position in the map:
https://github.com/scverse/spatialdata-io/blob/9a64e3457f9107b9cd8bd2518046e4c379fc49b6/s…
dawe updated
8 months ago
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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 scanpy.
- [ ] (option…
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I have Nanostring data from 3 slides. I was able to use Squidpy on each of them. I am wondering if Squidpy can read several slides simultaneously. Currently, I combined the datasets from several sli…
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**Describe the bug**
When trying to load VDJ data into environment with the "read_10x_vdj" function, it only loads the barcodes and none of the other information in the csv file. When checking the ad…
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Hi! Thanks for porting slingshot to python. I've been using this and it saves having to port single cell data back and forth between R and python, which is always nice.
I'd like to try to make this…
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@LucaMarconato when downloading the data set from the link in the notebook (https://s3.embl.de/spatialdata/spatialdata-sandbox/visium.zip) I think I get different data than the one used …
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Dear all,
I'm working mainly on Xenium data and there the segmentation delivered by the machine is not optimal. Therefore, reading the results from external tools would be great. Currently, `io.xen…
jwrth updated
7 months ago