CNV data of more than 100 genes using cBio portal web-interface, webservices or R package

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9.7 years ago

Khader Shameer 18k

Hello all,

I am using cBio to gather mutation statistics of more than 1000 genes.

I am hitting a small problem when I look for all CNVs reported in each study using cBIO portal.

For example: I am interested in looking for all CNVs ever reported for five different ovarian cancer studies. I have tried to explore it using HGNC gene list and noted that only 100 genes are allowed to search using the web interface.

I can't see a method / function / URL encoding to parse CNV data using your R package or the Web-service. May be this is doable using something very simple or may be am missing something.

Any help to extract genome-wide CNV data is really appreciated!

Thanks in advance !

genomics tcga cbio • 2.0k views

ADD COMMENT • link updated 2.3 years ago by Ram 43k • written 9.7 years ago by Khader Shameer 18k

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I have contacted cbio portal via their help page and have got no response, yet.

If I get an response - will post it here.

ADD REPLY • link updated 2.3 years ago by Ram 43k • written 9.7 years ago by Khader Shameer 18k

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@Khader Shameer

Did you find a way to use more than 100 genes in the cbioportal?

ADD REPLY • link 9.1 years ago by ivivek_ngs ★ 5.2k

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