[BioC] Which application to start BioConductor?

[Kevin R. Coombes]

Hi,

Because BioConductor is so large, it can be hard for new investigators 
(or older investigators who haven't used it regularly) to figure out 
where to start .  To help address this issue, we have developed an 
experimental tool that provides an interactive graphical overview of 
BioConductor.  The tool is available at
        http://bioinformatics.mdanderson.org/BioCycle
Just follow the link from that page to the "Interactive Flash circular 
graph".  The nodes in this graph represent different BioConductor 
packages, and the edges represent the "Depends" relationships.  Each 
node links to the full package documentation at bioconductor.org.  Under 
the same principle that we use for biological networks and pathways, it 
seems reasonable to assume that "hub nodes" are particularly important 
packages and might prove a good place to start. For instance, Biobase is 
the largest hub, with affy and limma fairly prominent secondary hubs.  
Reading about how the latter two packages work is probably a good place 
to start learning about how to apply BioConductor to microarrays.

Best,
    Kevin


cihan inan wrote:
> Well I am a biology student at university. and next year I will be a master
> student. I am planning to be in bioinformatics department. that's why I need
> to learn as much as I can. But at first I want to learn analysis about
> microarrays. from beginning to the end.  normalisation etc... I have 6
> months and I think it is enough to learn a lot of think about microarrays.
>
> 2010/1/6 James W. MacDonald <jmacdon at med.umich.edu>
>
>   
>> cihan inan wrote:
>>
>>     
>>> Hi all,
>>>
>>> I am new with bioconductor and I want to learn all apps. but I want to
>>> have
>>> a to do list. What's you opinion? What should I do? and which application
>>> must be the first to start?
>>>
>>>       
>> I seriously doubt you want to learn how to use all 353 packages. Perhaps
>> you could tell us what sort of data you have and what you are planning to do
>> with it?
>>
>> Best,
>>
>> Jim
>>
>>
>>
>>     
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>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> Douglas Lab
>> University of Michigan
>> Department of Human Genetics
>> 5912 Buhl
>> 1241 E. Catherine St.
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>
>
>
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