Can anyone suggest the good tool for identification of deregulated pathway by Multi-omic analysis using TCGA data?

I would like to find the deregulated pathway in cancer, I have done the gene enrichment analysis using gene expression data in pathview in R. However I do not know how to identify the deregulated pathway using SNV, CNV, and gene expression data belong to the same patient in the selected sample (you can say integrated analysis). Can anyone help in finding the right tool to do such job?

R tool or python would be better but web server will also work.

Thanks in advance