Jiang Feng

Thanks for your reply! It's really helpful. But I am also confused about which step needs phasing data. I downloaded the example data from https://zerkalo.curie.fr/partage/HiC-Pro/HiCPro_testdata_as.tar.gz . The _snps_CAST_129S1.vcf_ file in...

Thanks for your quick reply! I understand better now~ : ) Jiang

Thanks for your response! So each TF-gene pairs would have three lines (for direction prediction): "TF \t target \t 1" + "target \t TF \t 2" + "TF \t nontarget...

Thanks! Now I understand the index list. For my second question, you understand it correctly. In section 7.3 to do prediction, I think the "NEPDF_pathway" is the gene pairs histogram...

Got it! Thank you very much!

Thanks for your reply! I will have a try!

Hi, I noticed that train_with_labels_three_foldx_3fold_TF_two_labels.py should be used to predict the TF-target gene relationship, so I use this script to do the training on my own data. The test accuracy...

I edited the "get_xy_label_data_cnn_combine_from_database.py", then it runs well on example sc-RNA seq data. However, when I use it to run on my own sc-RNA seq data, it reported the same...

Thanks! I generate the h5 file with pd.HDFStore and it runs well. Another question is about the get_xy_label_data_cnn_combine_from_database.py scripts:  I noticed the annotation and removed the "[0:43261]" as described,...