Two of the R scripts used in our publications have been published as Shiny Apps and are available for use by scientists and the public.
If you wish to analyse the TCGA data to determine which pathways are enriched for gains or losses in genes grouped by signaling pathway, you are looking for HAPTRIG. 
If you want a tool to visualize regions of chromosomal gain or loss in different cancers, you are looking for CAIRN. 
In the US, a woman dies of ovarian cancer every 38 minutes. Consider helping us fight this disease.
The Stupack Lab
is a part of:
Division of Gynecologic Oncology
The Department of Pathology
A list of our Publications on Pubmed Here