pair information of microRNA and Targets prediction
1
2
Entering edit mode
@jrwangitriorgtw-3946
Last seen 10.2 years ago
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 ???????????????????????????????????????????? This email may contain confidential information. Please do not use or disclose it in any way and delete it if you are not the intended recipient.
microRNA RmiR microRNA RmiR • 1.1k views
ADD COMMENT
2
Entering edit mode
Laurent Gautier ★ 2.3k
@laurent-gautier-29
Last seen 10.2 years ago
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 > > ???????????????????????????????????????????? This email may contain > confidential information. Please do not use or disclose it in any way > and delete it if you are not the intended recipient. > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENT
2
Entering edit mode
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@stat.math.ethz.ch [mailto:bioconductor- bounces@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 > > ?????????????????????C???Y?????????????????????????????????????????? ?????K???N?????????? This email may contain > confidential information. Please do not use or disclose it in any way > and delete it if you are not the intended recipient. > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLY

Login before adding your answer.

Traffic: 876 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6