User: Jinyan Huang

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Jinyan Huang190
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Posts by Jinyan Huang

<prev • 19 results • page 1 of 2 • next >
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Answer: A: obtain the chromosome position/coordinates for probes on Affymetrix Human Exon 1
... Shirley, I have done the alignment using BLAT as you mentioned. But there are some tricks in it, for example, some probe sequence can map to multiple genome positions. Some cannot map to any position. Using different parameters will affect these results. When you prepare the files, the BLAT is ver ...
written 7.4 years ago by Jinyan Huang190
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Where is DEXSeq bioconductor package?
... When I download and install, I got this error. R CMD INSTALL DEXSeq_0.1.12.tar.gz * installing to library '~/R/x86_64-pc-linux-gnu-library/2.12' ERROR: dependency 'stringr' is not available for package 'DEXSeq' * removing '~/R/x86_64-pc-linux-gnu-library/2.12/DEXSeq' sessionInfo() R version 2.12. ...
dexseq written 8.3 years ago by Jinyan Huang190 • updated 8.3 years ago by Sean Davis21k
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Comment: C: microRNA hg build?
... 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 wrote: > Marc ...
written 8.6 years ago by Jinyan Huang190
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Comment: C: microRNA hg build?
... > 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 ...
written 8.6 years ago by Jinyan Huang190
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Answer: A: microRNA hg build?
... I think it is hg 19, but not very sure. On Sat, May 14, 2011 at 5:40 PM, 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 ...
written 8.6 years ago by Jinyan Huang190
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Comment: C: Is there annotation package for Affymetrix Human Exon 1.0 ST Array on bioconduct
... Hi Marc, Thanks for your suggestion. It is clear for this. On Fri, Feb 18, 2011 at 8:29 PM, Vincent Carey wrote: > It is also likely worth studying > > http://www.bioconductor.org/packages/2.7/bioc/vignettes/oligo/inst/d oc/V5ExonGene.pdf > > which shows how NetAffx annotations can ...
written 8.8 years ago by Jinyan Huang190
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Comment: C: R packages for position anotation?
... Hi Steve, Thanks for your suggestion. What I understand your suggestion is I shoud use exonsBy, intronsByTranscript, fiveUTRsByTranscrip, threeUTRsByTranscript separately. For example, if I want to check whether a position is in exon or not. I do as fellow. But this is just suitable for one positi ...
written 9.0 years ago by Jinyan Huang190
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Comment: C: Xmapcore package: check a position whether it is in a probe or probeset.
... It seems I need method range.in.probesets and range.in.probes. On Tue, Dec 14, 2010 at 10:31 AM, Jinyan Huang wrote: > Tim, > Thanks for your reply. > I have try probesets.in.range. It is not working for my purpose. Given > a snp, I want to check whether this snp is within a probeset o ...
written 9.0 years ago by Jinyan Huang190
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Comment: C: Xmapcore package: check a position whether it is in a probe or probeset.
... Tim, Thanks for your reply. I have try probesets.in.range. It is not working for my purpose. Given a snp, I want to check whether this snp is within a probeset or not. For example, for probeset, 3067144, the location is chr7:107002769-107002822 (-) I use probesets.in.range to check chr7:107002799. ...
written 9.0 years ago by Jinyan Huang190
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Xmapcore package: check a position whether it is in a probe or probeset.
... Dear all, Given a genome position (SNP), I want to know this position (SNP) is in a probe or probeset or not. Can Xmapcore have this function? The probe and probeset is for HuEx-1_0 array. Thanks. ...
probe xmapcore written 9.0 years ago by Jinyan Huang190

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