[BioC] human miRNA predicted/validated targets
Ranjani R [guest]
guest at bioconductor.org
Mon Jul 8 22:04:13 CEST 2013
Hi,
I am hoping to find an R package/downloadable resource for validated (and predicted) miRNA targets. I have already investigated a few sites : miRWalk (which is not downloadable in its entirety and has a limit on the number of miRNA you can feed into it's web form), tarBase (which does not seem to have been updated in a while) and miRecords. miRecords does have a downloadable excel spreadsheet with validated target information (and pubmed ID) - and has 2112 miRId -> Gene pairs.
Which is usually the methodology of choice for working with predicted/validated targets? I am concerned with using resources that may not be updated regularly -- or in downloading a file which may be a snapshot at a certain time.
Any guidance would be greatly appreciated.
Thanks,
Ranjani
-- output of sessionInfo():
R version 2.15.2 (2012-10-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] VennDiagram_1.6.0 edgeR_3.0.8 limma_3.14.4 DESeq_1.10.1 lattice_0.20-15 locfit_1.5-9.1
[7] Biobase_2.18.0 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] annotate_1.36.0 AnnotationDbi_1.20.7 DBI_0.2-7 genefilter_1.40.0 geneplotter_1.36.0
[6] IRanges_1.16.6 parallel_2.15.2 RColorBrewer_1.0-5 RSQLite_0.11.4 splines_2.15.2
[11] stats4_2.15.2 survival_2.37-4 tools_2.15.2 XML_3.98-1.1 xtable_1.7-1
--
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