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scverse / squidpy_notebooks

Tutorials for Squidpy
https://squidpy.readthedocs.io/en/stable/
MIT License
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Create tutorial_vizgen #93

Closed dineshpalli closed 2 years ago

dineshpalli commented 2 years ago

Add tutorial_vizgen to download, read, quality control of Vizgen dataset

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giovp commented on 2022-06-08T07:37:06Z ----------------------------------------------------------------

please use proper separation of section, e.g. here make it smaller and make bigger title for the QC and normalization section


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giovp commented on 2022-06-08T07:37:07Z ----------------------------------------------------------------

use smaller values here. Like 50 and 50


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giovp commented on 2022-06-08T07:37:07Z ----------------------------------------------------------------

Install scikit-misc package as it is used for Seurat_v3, a toolkit for single cell genomics. This is used to identify the highly variable genes.

You may have to install scikit-misc package for highly variable genes identification.


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giovp commented on 2022-06-08T07:37:08Z ----------------------------------------------------------------

remove "The spatial relations of the data were represented by the embedded points." It's false, where did you find it?

also, remove this

"

In this case, the fields of view which are the technical batches blends well with the UMAP, which implies that the batch effect is potentially low. If otherwise, this can be amended with the batch effect correction methods.

"

and remove the fov visualization


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giovp commented on 2022-06-08T07:37:09Z ----------------------------------------------------------------

remove rank_genes_groups section, not important.


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giovp commented on 2022-06-08T07:37:10Z ----------------------------------------------------------------

explicit that you are using mode generic and method e.g. delaunay or knn


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giovp commented on 2022-06-08T07:37:10Z ----------------------------------------------------------------

Line #16.        img=False,

do you need to specify image=False or it works also without? if it works without, remove


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giovp commented on 2022-06-08T07:37:11Z ----------------------------------------------------------------

for the spatial_scatter plot, show only some categories with groups=["0","1","3"]


giovp commented 2 years ago

closed in favour of #96 .

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