[BioC] Genes, their domains, and a list of superimposed mutations
Martin Morgan
mtmorgan at fhcrc.org
Fri Aug 30 13:52:02 CEST 2013
On 08/29/2013 06:29 AM, Gabriele [guest] wrote:
>
> Dear Bioconductor mailing list,
>
> I was wondering if anyone knows whether there is any package to plot figures with a given gene, its domains, and symbols from a list of pre-specified mutations, something like what is seen in the cBio portal (http://www.cbioportal.org/public-portal/index.do) when one looks for mutations, or in COSMIC (see this example: http://cancer.sanger.ac.uk/cosmic/gene/analysis?ln=BRAF#histo )... I haven't found anything although I did my research...
>
Not a detailed answer to your question, but I'd look at Gviz (which has an
excellent vignette) and ggbio. Martin
> Thanks!
>
> -- output of sessionInfo():
>
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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