squidpy_notebooks
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scverse
Tutorials for Squidpy
Following the same jupyter notebook (tutorial_visium_hne.ipynb) with the same tutorial data but got the following error: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In[10], line 6 1 sq.gr.ligrec( 2...
Hi there, Thank you for the tutorial! I was just running through the example data, and encountered this error at: ``` # calculate features for different scales (higher value means...
``` alan@pop-os:~/Documents/github/imaging/squidpy_notebooks/ (main) $ grep -r environment.yml tutorials/tutorial_mibitof.ipynb: "`environment.yml `_." tutorials/tutorial_seqfish.ipynb: "`environment.yml `_." tutorials/tutorial_visium_hne.ipynb: "`environment.yml `_." tutorials/tutorial_visium_fluo.ipynb: "`environment.yml `_." tutorials/tutorial_slideseqv2.ipynb: "`environment.yml `_." tutorials/tutorial_imc.ipynb: "`environment.yml `_." tutorials/tutorial_fouri.ipynb: "`environment.yml `_." tutorials/tutorial_merfish.ipynb: "`environment.yml...
Hi, Could you guys please update the version of Tangram to 1.0.3 in this [yaml](https://github.com/scverse/squidpy_notebooks/blob/main/envs/tangram_environment.yml) file? Thank you! Best, Shreya
CC @giovp @LLehner The 10x team reviewed the Xenium notebook and found it very useful! (Btw, it's ready to merge https://github.com/scverse/squidpy_notebooks/pull/125). They suggested to consider two improvements. - [ ]...
A first draft tutorial for calculating niches with squidpy. To be updated, as updates are made to https://github.com/scverse/squidpy/pull/831.
An updated Xenium tutorial for analysis using Squidpy, but instead of only working with `anndata`, `spatialdata` is used. @LucaMarconato please let me know if things should be added. So far...
Just cloned the repo and noticed that it was taking quite some time, downloading 550 MB for a fairly low-LOC repo: I wonder if there's any merit towards switching to...