[BioC] pair information of microRNA and Targets prediction

[jrwang at itri.org.tw]

Dear michael:

Thanks for your help.  I am testing this package.  It seems need to recompile with new version of R.  This is what I got.

>library(CORNA)
Loading required package: biomaRt
Loading required package: GEOquery
Loading required package: RCurl

Attaching package: 'GEOquery'


        The following object(s) are masked from package:Biostrings :

         dataTable 

Loading required package: XML
Warning message:
package 'CORNA' was built under R version c(2, 4, 0) and help will not work correctly
Please re-install it 


Weihsin Wang, Ph.D.
Bioinformatics Core Lab.,
Biomedical Engineering Research Lab.,
Industrial Technology Research Institute
TEL:886-3-5913689
FAX: 886-3-5820445

________________________________________
寄件者: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] 代表 michael watson (IAH-C) [michael.watson at bbsrc.ac.uk]
寄件日期: 2010年02月26日 下午 04:26
收件者: 'Laurent Gautier'; bioconductor at stat.math.ethz.ch
主旨: Re: [BioC] pair information of microRNA and Targets prediction

Hi

We published an R package early in 2009 which may help you:

http://bioinformatics.iah.ac.uk/software/corna

Wu X, Watson M: CORNA: testing gene lists for regulation by microRNAs. Bioinformatics 2009, 25(6):832-833.

CORNA can download data directly from miRBase targets (now called Microcosm targets) but this hasn't been updated in a while.  CORNA can, though, take any generic list of miR:gene target pairs and use that instead.

Thanks

Mick Watson
Head of Bioinformatics
Institute for Animal Health

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Laurent Gautier
Sent: 26 February 2010 08:20
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] pair information of microRNA and Targets prediction

Hi Weihsin,

My understanding is that microRNA only contains example data (so the
exact version for the data source is of moderate importance). The only
package containing database data might be "RmiR.Hs.miRNA" (dependency of
RmiR). The version might be indicated in the source code (check the SVN
repository for that bioconductor package), otherwise the author should
be contacted.


Laurent




On 2/26/10 11:34 AM, jrwang at itri.org.tw wrote:
>
> I am currently working on some microRNA experiments.  I would like to
> find the relation between microRNA and predicted targets from
> targetscan and miRanda.  To do it from scratch will be last choice. I
> look the currently available packages.  Two packages, RmiR and
> microRNA, seems fitting my purpose.  However, there are a few
> questions after I use the packages. 1. What is the version of mirbase
> used in most current microRNA package? 2.  Similar to question 1,
> what is the version of data from various resources used in RmiR?  Is
> there a way to find out?
>
> Thanks
>
>> sessionInfo()
> R version 2.10.1 (2009-12-14) i386-pc-mingw32
>
> locale: [1] LC_COLLATE=Chinese_Taiwan.950
> LC_CTYPE=Chinese_Taiwan.950    LC_MONETARY=Chinese_Taiwan.950
> LC_NUMERIC=C                   LC_TIME=Chinese_Taiwan.950
>
> attached base packages: [1] stats     graphics  grDevices utils
> datasets  methods   base
>
> other attached packages: [1] microRNA_1.4.0       Rlibstree_0.3-2
> Biostrings_2.14.12   IRanges_1.4.11       RmiR_1.2.0
> RSVGTipsDevice_1.0-1 RmiR.Hs.miRNA_1.0.6  RSQLite_0.8-3
> DBI_0.2-5
>
> loaded via a namespace (and not attached): [1] AnnotationDbi_1.8.1
> Biobase_2.6.1
>
>
> Weihsin Wang, Ph.D. Bioinformatics Core Lab., Biomedical Engineering
> Research Lab., Industrial Technology Research Institute
> TEL:886-3-5913689 FAX: 886-3-5820445
>
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