microRNA hg build?
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 10.3 years ago
Hi, I wanted to find the coordinates/locations for microRNA targets. I use 'hsTargets' in the package to find these. How can I find information on which build (hg18/hg19 etc) was used for these locations? thanks. [[alternative HTML version deleted]]
microRNA microRNA • 1.9k views
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Jinyan Huang ▴ 190
@jinyan-huang-4157
Last seen 10.3 years ago
I think it is hg 19, but not very sure. On Sat, May 14, 2011 at 5:40 PM, Tim Smith <tim_smith_666 at="" yahoo.com=""> wrote: > Hi, > > I wanted to find the coordinates/locations for microRNA targets. I use > 'hsTargets' in the package to find these. How can I find information on which > build (hg18/hg19 etc) was used for these locations? > > thanks. > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 8.4 years ago
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Hi Tim, Which package? SessionInfo() ? Marc On 05/14/2011 08:40 AM, Tim Smith wrote: > Hi, > > I wanted to find the coordinates/locations for microRNA targets. I use > 'hsTargets' in the package to find these. How can I find information on which > build (hg18/hg19 etc) was used for these locations? > > thanks. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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> library("microRNA") > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] microRNA_1.8.0 loaded via a namespace (and not attached): [1] Biobase_2.10.0 Biostrings_2.18.0 IRanges_1.8.9 On Mon, May 16, 2011 at 5:57 PM, Marc Carlson <mcarlson@fhcrc.org> wrote: > SessionInfo() [[alternative HTML version deleted]]
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Hi Jinyan, Instead of using the microRNA package, have you considered using the mirbase.db or the targetscan packages? The reason I suggest that is that I think it is more up-to date on account of being a proper annotation package. After contacting James Reid (who is the maintainer of both the mirbase.db and the targetscan packages), I can tell you that mirbase.db is based on hg19 but that the targetscan packages are probably based on hg18. In both cases the data just represents the most recent information available. Below are some links that can help you learn more about these other packages: http://www.bioconductor.org/packages/release/data/annotation/html/mirb ase.db.html http://www.bioconductor.org/packages/release/data/annotation/html/targ etscan.Hs.eg.db.html Marc On 05/16/2011 09:06 AM, Jinyan Huang wrote: > > library("microRNA") > > sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] microRNA_1.8.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 Biostrings_2.18.0 IRanges_1.8.9 > > On Mon, May 16, 2011 at 5:57 PM, Marc Carlson <mcarlson@fhcrc.org> <mailto:mcarlson@fhcrc.org>> wrote: > > SessionInfo() > > [[alternative HTML version deleted]]
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Marc, Thank you for your information. I prefer hg19. In my analysis, I have a list snp. I want to check whether this snp is in the microRNA in the binding sites or not. I do not know whick packages is better. Thanks. On Tue, May 17, 2011 at 10:41 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Marc
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I was wondering if anybody has used arrayQualityMetrics for analyzing Affymetrix miRNA data? If not, could anybody suggest a BioC package to do this? Thanks in advance. Som. [[alternative HTML version deleted]]
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Hi Tim / Jinyan, now I understand what you are trying to do. You probably want to use the rtracklayer library to access the hg19 targetscan tables provided by ucsc: library("rtracklayer") session <- browserSession() genome(session) <- "hg19" query <- ucscTableQuery(session, "TS miRNA sites", genome(session)) print(query) tableNames(query) tsCoords <- track(query) print(tsCoords, n=3) HTH, J. On 05/17/2011 10:48 PM, Jinyan Huang wrote: > Marc, > > Thank you for your information. I prefer hg19. In my analysis, I have > a list snp. I want to check whether this snp is in the microRNA in the > binding sites or not. I do not know whick packages is better. > > Thanks. > > On Tue, May 17, 2011 at 10:41 PM, Marc Carlson<mcarlson at="" fhcrc.org=""> wrote: >> Marc > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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sorry, the last statement should be just 'print(tsCoords)', remove the n=3. J. On 05/18/2011 02:01 PM, James F. Reid wrote: > Hi Tim / Jinyan, > > now I understand what you are trying to do. > You probably want to use the rtracklayer library to access the hg19 > targetscan tables provided by ucsc: > > library("rtracklayer") > session <- browserSession() > genome(session) <- "hg19" > query <- ucscTableQuery(session, "TS miRNA sites", genome(session)) > print(query) > tableNames(query) > tsCoords <- track(query) > print(tsCoords, n=3) > > HTH, > J. > > > On 05/17/2011 10:48 PM, Jinyan Huang wrote: >> Marc, >> >> Thank you for your information. I prefer hg19. In my analysis, I have >> a list snp. I want to check whether this snp is in the microRNA in the >> binding sites or not. I do not know whick packages is better. >> >> Thanks. >> >> On Tue, May 17, 2011 at 10:41 PM, Marc Carlson<mcarlson at="" fhcrc.org=""> wrote: >>> Marc >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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