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Deployed online at:
https://arraycgh.shinyapps.io/Copy_Number_Explorer/
https://arraycgh.shinyapps.io/Copy_Number_Explorer_Survival/
Copy Number Explorer is a data mining tool for cancer researchers interested in the structural and copy number changes.
Huge volumes of genomics data from nearly every cancer type are now freely available and several online databases have begun to collate and store this information. However, current tools focus on individual gene queries rather than chromosomal and region-based queries more relevant to some researchers. Copy Number Explorer creates interactive CNV frequency, GISTIC-style and breakage frequency plots from public (or your own) data. The program is written in R and Perl and can be deployed online using ShinyApps.io .
Copy Number Explorer is available under the GNU public license (GPL-3).
Check the Wiki for details on how to run your own Copy Number Explorer instance.
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User Reviews
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The tool in general is good, BUT it contains a major problem regarding the survival analysis, which makes the p-values and the curves may not be accurate. The problem: the code sums the time for the death with the time of the follow up, which are the same number and this means when the patient is dead, the death time will be doubled. To solve this quickly, the user should change the attached survival data by putting 0s instead of the numbers in the days to death column. So I am asking the author to change this to solve this issue.