scanpy-tutorials
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Scanpy Tutorials.
Couldn't find anything in exisitng/closed issue so I asked here. Thank you for implementing those concise yet comprehensive tutorials. In [Visium data processing tutorial](https://scanpy-tutorials.readthedocs.io/en/latest/spatial/basic-analysis.html), no scaling was done before PCA...
Here's my first draft of using some external plotting tools, including interactive ones. @falexwolf is this what you were thinking of (mentioned in #460)? Or did you want specifically just...
Hi, is there data_processed.h5ad existed in somewhere? The scanpy workshop day 2 has to analyze it. I can only find GEO file, or should I create it myself. Thanks.
**To Reproduce** Run https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html with the current [scanpy master branch](https://github.com/scverse/scanpy/commit/b6d0fc4873b800a02209cc956891deeb6ba63b0d) and the results of marker gene plotting do not match the table. For example `IL7R` is not ranked highly in...
Hey, I really don't know if this could be called an issue. Since in the paper justifying [square root normalization ](https://www.biorxiv.org/content/10.1101/770388v3.full)for visualization and clustering? and the [Pearson residue](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02451-7) normalizes and...
There are a lot of Chinese developers who need scanpy's Chinese documentation, so I want to translate the documentation into Chinese version, how do I translate, contribute, and merge it
typo
'Take a look at tools in the external API or at the ecoystem page to get a start with other tools.' should be 'Take a look at tools in the...
Hi, which scanpy version has the normalize_geometric function for citeseq data? I'm running: ``` sc.logging.print_versions() scanpy==1.5.2.dev24+g83844013 anndata==0.7.3 umap==0.4.4 numpy==1.18.5 scipy==1.4.1 pandas==1.0.5 scikit-learn==0.23.1 statsmodels==0.11.1 ``` thanks!
see https://github.com/theislab/scanpy/issues/1283#issuecomment-645269898 @LuckyMD we should change the tutorials instead of going back, because [louvain is deprecated](https://github.com/vtraag/louvain-igraph/blob/b3a8e6be2c3916e4082e8171a31e8752317e4c5c/src/__init__.py#L63-L66): > This package has been superseded by the `leidenalg` package and will no longer...
@giovp, input 8 of the spatial integration tutorial currently looks like this: ```python adata_spatial = adata_spatial_anterior.concatenate( adata_spatial_posterior, batch_key="library_id", uns_merge="unique", batch_categories=[ k for d in [ adata_spatial_anterior.uns["spatial"], adata_spatial_posterior.uns["spatial"], ] for k,...