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JieZheng-ShanghaiTech / HiCoEx

A supervised learning model based on Graph Neural Network to predict gene co-expression from chromatin contacts
MIT License
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Cannot find GSE50244_TMM_NormLength.xlsx #1

Open DylanMannKrzisnik opened 1 year ago

DylanMannKrzisnik commented 1 year ago

Hello,

I cannot find the file GSE50244_TMM_NormLength.xlsx, which seems to be required to run run_islet.sh. I was able to find related files at GEO accession number GSE50244, but not the excel file just mentioned.

From the parser commands in line 51 of 01_gene_expression_islet.py, it seems that this file can be found in the Xena Browser. Is there a dataset name or label that can be used to retrieve GSE50244_TMM_NormLength.xlsx from Xena Browser?

Thank you!

pearlstory commented 1 year ago

Hello,

I cannot find the file GSE50244_TMM_NormLength.xlsx, which seems to be required to run run_islet.sh. I was able to find related files at GEO accession number GSE50244, but not the excel file just mentioned.

From the parser commands in line 51 of 01_gene_expression_islet.py, it seems that this file can be found in the Xena Browser. Is there a dataset name or label that can be used to retrieve GSE50244_TMM_NormLength.xlsx from Xena Browser?

Thank you!

Hi,

This file is actually the file named GSE50244_Genes_counts_TMM_NormLength_atLeastMAF5_expressed.txt.gz in GSE50244. You just need to convert the .txt format as .xlsx and rename it.