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bryanhe / ST-Net

Deep learning on histopathology images.
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ensembl.tsv #7

Closed suke18 closed 3 years ago

suke18 commented 3 years ago

Hello Bryan,

I recently read your work stnet and am very interested in the model. I tried your command "python3 -m stnet prepare spatial" but there is no ensembl.pkl or ensembl.tsv files in the utils folder.

Thanks, Kenong

suke18 commented 3 years ago

solved

yongshuo-Z commented 3 years ago

@suke18 Hi, I met the same issue. Would you mind sharing the solution?

suke18 commented 3 years ago

2 I think this thread might answer your question. I downloaded it from https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=md_ensembl_id&status=Approved&status=Entry%20Withdrawn&hgnc_dbtag=on&order_by=gd_app_sym_sort&format=text&submit=submit. I forget where to download the .pkl but it is on my laptop for some reason.

yongshuo-Z commented 3 years ago

2 I think this thread might answer your question. I downloaded it from https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=md_ensembl_id&status=Approved&status=Entry%20Withdrawn&hgnc_dbtag=on&order_by=gd_app_sym_sort&format=text&submit=submit. I forget where to download the .pkl but it is on my laptop for some reason.

Thanks a lot! Solved the .tsv. Could you share the .pkl if possible?

johnchen99 commented 2 years ago

2 I think this thread might answer your question. I downloaded it from https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=md_ensembl_id&status=Approved&status=Entry%20Withdrawn&hgnc_dbtag=on&order_by=gd_app_sym_sort&format=text&submit=submit. I forget where to download the .pkl but it is on my laptop for some reason.

Thanks a lot! Solved the .tsv. Could you share the .pkl if possible?

Hi, may I know if you've a solution for ensembl.pkl?