scverse squidpy issues - Githubissues

scverse / squidpy

Spatial Single Cell Analysis in Python

https://squidpy.readthedocs.io/en/stable/

BSD 3-Clause "New" or "Revised" License

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issues

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import squidpy and get an error

#915 xyuechen closed 1 week ago
1
[pre-commit.ci] pre-commit autoupdate

#914 pre-commit-ci[bot] opened 1 week ago
0
Read Xenium v3 data error

#913 2613df closed 1 week ago
0
Delegate plots to spatialdata-plot

#912 LucaMarconato opened 2 weeks ago
4
Update spatialdata dependency

#911 melonora closed 2 weeks ago
1
Spatially Correlated Genes

#910 jamesboot closed 1 week ago
3
[pre-commit.ci] pre-commit autoupdate

#909 pre-commit-ci[bot] closed 2 weeks ago
0
Add parameter to `sliding_window` to end up with windows of (approximately) same number of cells

#908 timtreis opened 2 weeks ago
2
New xarray release (v2024.10.0) is breaking squidpy install

#907 ajulienla closed 1 week ago
2
Visium observation with NaN metadata

#906 jychien opened 3 weeks ago
1
Extend monkeybread neighbourhood to include n>1 cells

#905 timtreis opened 3 weeks ago
1
[pre-commit.ci] pre-commit autoupdate

#904 pre-commit-ci[bot] closed 3 weeks ago
0
numpy 2.0 and python >= 3.10 compatibility changes

#903 timtreis closed 2 weeks ago
0
Numpy 2 Compat

#902 ilan-gold closed 2 weeks ago
0
Add SpaGFT-like method for identification of SVGs

#901 timtreis opened 1 month ago
0
[pre-commit.ci] pre-commit autoupdate

#900 pre-commit-ci[bot] closed 3 weeks ago
0
How to draw co_occurrence plot with specific distance in x-axis?

#899 Zhaowado opened 1 month ago
0
Sparse matrix fix

#898 alam-shahul closed 1 month ago
1
How to combine the image from ImageCollection object with a anndata object?

#897 HelloWorldLTY closed 1 month ago
4
Update .pre-commit-config.yaml

#896 LLehner closed 1 month ago
0
How to save the iamge as svs or png?

#895 HelloWorldLTY closed 1 month ago
1
CosMx FOVs being skipped

#894 jamesboot opened 1 month ago
1
Tutorial for Visium applicable to Visium HD?

#893 spatts14 closed 1 month ago
3
`TypeError` when going through the Visium tutorial

#892 matt-sd-watson closed 1 month ago
1
Fix sparse matrix interactions in `sq.gr.utils`.

#891 alam-shahul closed 1 month ago
3
`squidpy==1.6.1` not compatible with `anndata>=0.11.0`

#890 alam-shahul closed 1 month ago
0
Mapping of Xenium 5k data

#889 shanggutianzhen opened 2 months ago
5
is there a way to view older versions of the documentation over on readthedocs?

#888 owenwilkins closed 2 months ago
3
Edge correction in `squidpy.gr.ripley`?

#886 zsfrbkv opened 2 months ago
1
[pre-commit.ci] pre-commit autoupdate

#885 pre-commit-ci[bot] closed 1 month ago
0
[doc improvment] inconsistent usage of img_key and img_res_key in code base

#884 TTTPOB opened 2 months ago
1
add release note

#883 giovp closed 2 months ago
0
remove 3.9 support, fix precommit, release note

#882 giovp closed 2 months ago
0
fix precommit

#881 giovp closed 2 months ago
0
[pre-commit.ci] pre-commit autoupdate

#880 pre-commit-ci[bot] closed 2 months ago
0
Add SpatialLeiden as clustering method

#879 timtreis opened 2 months ago
0
Expected Width error calculate_image_features

#878 qiutip closed 3 months ago
0
remove napari from install

#877 giovp closed 2 months ago
1
Infer parameters in `sq.gr.spatial_neighbors` when only one choice

#876 timtreis opened 3 months ago
1
Catch-all: XYZ doesn't work with `SpatialData`

#875 timtreis opened 3 months ago
4
Incompatibility with spatialdata objects on plotting features by using sq.pl.spatial_scatter

#874 joonlee3 closed 2 months ago
1
Is Xenium data can be 3D visualization/ can the Stardist do 3D segmentation/ is squidy able to crop image for further analysis

#873 Yifan-debug closed 3 months ago
2
Import from QuPath or CODEX Dataset

#872 andreevg04 opened 3 months ago
1
Ligand-receptor plot always report Error

#871 ryrl970311 opened 3 months ago
5
sq.gr.ripley() cost too much memory

#870 wangjiawen2013 opened 3 months ago
1
Fix links to references

#869 LLehner closed 3 months ago
1
Update ```var_by_distance```

#868 LLehner closed 3 months ago
0
No matching definition for argument type

#867 wangjiawen2013 opened 3 months ago
3
MVP for morpohology module

#866 timtreis opened 3 months ago
2
`_pickle.UnpicklingError: pickle data was truncated` running ligrec

#865 Rafael-Silva-Oliveira closed 3 months ago
1