[BioC] SomaticSignatures

Julian Gehring julian.gehring at embl.de
Mon Mar 24 09:25:37 CET 2014

Hi Hasif,

For this, the 'mutationContext' should be all you need.  As Steve
mentioned, the vignette of the package covers a real-life example with
all the relevant steps.

Best wishes

On 22/03/14 23:52, Steve Lianoglou wrote:
> Hi,
> On Sat, Mar 22, 2014 at 2:13 PM, hasif [guest] <guest at bioconductor.org> wrote:
>> Hi there,
>>> I am a Post-doc student started analyzing human genome data few days
>>> back. My aim is to find UVA signature mutations. i have done variant
>>> calling by GATK and was wondering how i can extract signatures using
>>> these call without using much programming (as I am a biologist working
>>> in Bioinformatics field). while doing search on web i came
>>> across Package â EURO ~SomaticSignaturesâ EURO (tm). i have some questions
>>> can you please suggest what can help me in handling this package?
>>> My first aim is to use my data and find sequence context of  these variants
>>> please suggest me any easy guide to start with
> Have you read through the rather extensive looking vignette?
> http://www.bioconductor.org/packages/devel/bioc/vignettes/SomaticSignatures/inst/doc/SomaticSignatures-vignette.pdf

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