squidpy
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Spatial Single Cell Analysis in Python
## Description I have changed the relative coordinate to exact coordinate in the `feature_segmentation` function. There are two reasons: 1. because of the normalization of "np.max(y) - np.min(y)" in denominator,...
Do you have any recommendations about the concatenation of Visium spots from multiple samples into a single anndata object? Is it valid to analyse them together using the single-cell pipeline?...
Don't sorted label_rankge keys according to issues https://github.com/scverse/squidpy/issues/560#issuecomment-1152842944
Hello, I get the following error while trying to replicate the Nanostring tutorial. I tried installing both the 'dev' version from Github as well as Squidpy 1.2.2. ``` KeyError Traceback...
## Description ... ## Minimal reproducible example ```python ... ``` ## Traceback ```pytb ... ``` ## Version ...
## Description ...hello I am struggling with 2 spatial transcriptomics data to compare, but the 2 tissues were spoted perpendicular to each other I dont know how to pivot the...
hello again, do you plan to integrate CODEX data in squidpy package ? Many thanks Sophie ...
## Description hello again :) I am trying to add a point layer to napari in interactive mode. I follow these indications to add cells positions that I got with...
Hi, when I plot leiden clusters with sc.pl.spatial(adata[adata.obs['sample']=="C8"],library_id="C8",color=['n_genes_by_counts','leiden']), the color of each leiden cluster became disordered. There are 3 samples (C6, C7, C8) in my anndata object and was clustered...
when I use sq.pl.ligrec to plot the interaction, the axis wasn't ordered by leiden number, but by dict order. I changed the order of the leiden categories by: ```python adata.obs['leiden']...