[BioC] pair information of microRNA and Targets prediction

[Laurent Gautier]

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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