SpaGCN

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target_cluster, x/y_pixel and nbr_domians in Identify SVGs section

2

Hi Dr. Hu, Sorry for new questions. I am running SpaGCN for identifying SVGs using my spatial data. There are some troubles stopped me to get through this section. 1....

lifan18

I see functions Moran_I and Geary_C in `calculate_moran_I.py`. But I don't see how to use them in tutorial. I also don't see any comments

QingJun3

Dear Dr. Hu, Thank you for making SpaGCN available. When I trying reproducing your SpaGCN, I have some problems about data. Could you give me your ST h5ad data and...

zhaofangyuan98

Dear Dr. Hu, I ran my data with SpaGCN and found this software is good for Spatial transcriptomic data generated by one chip. On the other hand, the results from...

lifan18

spg.calculate_adj_matrix is making all Nan with our own FFPE histology image

1

Hello, Thank you for making SpaGCN available to community. When I am trying SpaGCN with my own FFPE histology images on a 10X Visum data, the spg.calculate_adj_matrix is producing all...

galib36

Reproduction issue on tutorial

1

Hi Jian, Initially, I wasn't able to reproduce the same or similar results with your reported ones in the tutorial. Then I tried environment 3 you listed on the readme,...

JiayuanDing100

how to use detect_spatial_domains_ez_mode without histology image

1

Hi Dr. Hu! I am reading the SpaGCN Easy Mode Tutorial and I wish to know how to use the function "detect_spatial_domains_ez_mode" if users do not have a histology image?...

linpei26

Adjacency matrix of DLPFC 151673

3

Dear Dr. Hu, Thanks for providing your adjacency matrix, using it, result can be reproduced perfectly ! But I have a problem, I compare the two adj.csv, it has huge...

xiao-kong-long

NotADirectoryError

2

Hello developer! I have tried configure an environment for SpaGCN on ubuntu server, however, three ways to installation in tutorial are not worked. And all of them report same errors,...

xiao-kong-long

Reproduction issue on tutorial: error at the steps with louvain algorithm

2

Hi Dr. Hu, I want to reproduce results via SpaGCN in the given tutorial (https://github.com/jianhuupenn/SpaGCN/blob/master/tutorial/tutorial.ipynb). However, I got error “BaseException: Could not construct partition: vector” which seems in the steps...

huimin230