Re: [Bioc-devel] ggbio: gridExtra 2.0.0 breaks import

gt; - R :: 3.2.1 > > - ggbio :: 1.16.0 > > - gridExtra :: 2.0.0 > > > > I'm not the maintainer of ggbio but I did just check in a fix for this in > release and devel. > Dan > > > > Best wishes > > Julian > > > > ___________

Re: [Bioc-devel] ggbio 1.13.11 fails to load due to namespace change in IRanges

36] plyr_1.8.1 proto_0.3-10 > RColorBrewer_1.0-5 Rcpp_0.11.2 RCurl_1.95-4.1 > [41] reshape_0.8.5reshape2_1.4 > Rsamtools_1.17.31RSQLite_0.11.4 rtracklayer_1.25.13 > [46] S4Vectors_0.1.2 scales_0.2.4 sendmailR_1.1-2 >

Re: [Bioc-devel] Namespace issues with ggbio 1.13.6 from AnnotationDbi 1.27.6 not exporting 'cols'

ave to change anything. > > Dan > > > ----- Original Message - > > From: "Tengfei Yin" > > To: "Leonardo Collado Torres" > > Cc: bioc-devel@r-project.org > > Sent: Thursday, May 22, 2014 12:10:29 PM > > Subject: Re: [Bioc-devel] Nam

Re: [Bioc-devel] Namespace issues with ggbio 1.13.6 from AnnotationDbi 1.27.6 not exporting 'cols'

s_0.0.6 > [46] scales_0.2.4 sendmailR_1.1-2 splines_3.1.0 > [49] stats4_3.1.0 stringr_0.6.2survival_2.37-7 > [52] tools_3.1.0 VariantAnnotation_1.11.5 XML_3.98-1.1 > [55] XVector_0.5.6zlibbioc_1.11.1 > >

Re: [Bioc-devel] IRanges:::safeExplode

Thanks a lot! Tengfei On Wed, Apr 23, 2014 at 5:34 PM, Hervé Pagès wrote: > Hi Tengfei, > > > On 04/23/2014 02:28 PM, Tengfei Yin wrote: > >> Hi all, >> >> I found IRanges:::safeExplode() removed, is there any recommended >> alternative method I s

[Bioc-devel] IRanges:::safeExplode

Hi all, I found IRanges:::safeExplode() removed, is there any recommended alternative method I should use to replace it? thanks Tengfei -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite #208 Cambridge, MA 02138 (617) 866-0446 [[alternative HTML

Re: [Bioc-devel] seqlevelsStyle<- doesn't work for GRanges object

Thanks a lot, it works! cheers Tengfei On Fri, Apr 11, 2014 at 5:37 AM, Hervé Pagès wrote: > Hi Tengfei, > > Should be fixed in GenomicRanges 1.15.45 > > > On 04/10/2014 03:29 PM, Tengfei Yin wrote: > >> forget to say "thank you" in the end :) >>

Re: [Bioc-devel] seqlevelsStyle<- doesn't work for GRanges object

forget to say "thank you" in the end :) On Thu, Apr 10, 2014 at 6:22 PM, Tengfei Yin wrote: > Hi all, > > "seqlevelsStyle<-" method does work for me in devel-branch, I haven't dig > into it yet, please check out the code below and its output. > &g

[Bioc-devel] seqlevelsStyle<- doesn't work for GRanges object

ges: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicRanges_1.15.44 GenomeInfoDb_0.99.31 IRanges_1.21.45 [4] BiocGenerics_0.9.3 loaded via a namespace (and not attached): [1] stats4_3.1.0 XVector_0.3.7 -- Tengfei Yin, Ph

Re: [Bioc-devel] ggbio: Support of object inheriting from 'GRanges'

GRanges and VRanges? > > Best wishes > Julian > > ___________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Tengfei Yin, PhD Seven Bridges Genomics sbgenomics.com 625 Mt. Auburn St. Suite

Re: [Bioc-devel] ggbio: autoplot(TranscriptDb) slow at certain regions

ei On Thu, Apr 11, 2013 at 2:36 PM, Tengfei Yin wrote: > Hi Julian, > > I confirmed the issue, thanks a lot, I will keep you updated on the fix. > > Tengfei > > On Thu, Apr 11, 2013 at 2:05 PM, Julian Gehring > wrote: >> Hi, >> >> Using the 'autoplot&#

Re: [Bioc-devel] ggbio: autoplot(TranscriptDb) slow at certain regions

plyr_1.8 > [19] proto_0.3-10RColorBrewer_1.0-5 RCurl_1.95-4.1 > [22] reshape2_1.2.2 Rsamtools_1.13.1RSQLite_0.11.2 > [25] rtracklayer_1.21.0 scales_0.2.3stats4_3.1.0 > [28] stringr_0.6.2 tools_3.1.0 VariantAnnotation_1.7.4 >

Re: [Bioc-devel] [VariantAnnotation] segfault thrown when scan header for VCF files out of GATK pipeline

ei On Tue, Feb 19, 2013 at 2:17 PM, Tengfei Yin wrote: > Hi Martin, > > Thanks a lot for the quick help! > > I will get back to you off-list with the ouput and vcf header after trying > what you suggested. > > Tengfei > > On Tue, Feb 19, 2013 at 1:58 PM, Martin Mo

Re: [Bioc-devel] [VariantAnnotation] segfault thrown when scan header for VCF files out of GATK pipeline

Hi Martin, Thanks a lot for the quick help! I will get back to you off-list with the ouput and vcf header after trying what you suggested. Tengfei On Tue, Feb 19, 2013 at 1:58 PM, Martin Morgan wrote: > On 02/19/2013 11:44 AM, Tengfei Yin wrote: > >> Hi , >> >> I am

[Bioc-devel] [VariantAnnotation] segfault thrown when scan header for VCF files out of GATK pipeline

RSQLite_0.11.2 [10] rtracklayer_1.19.9 stats4_3.0.0tools_3.0.0 [13] XML_3.95-0.1zlibbioc_1.5.0 -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 [[alternative HTML version deleted]] ___

Re: [Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

s the argument to > exonRankAttributeName... > > > Also, I am just now checking in a solution to the other inconvenience that > you reported earlier (to the devel branch). So look for an update to > appear very soon (or DL it from svn if you are impatient). Please let me > know i

Re: [Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

he exons for a given transcript, which can > render them difficult (or impossible) to use for transcript work. But for > these specifications, that information is "optional". > > > Marc > > > > > On 02/06/2013 09:46 PM, Tengfei Yin wrote:

[Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

species = "Glycine max", dataSource = "http://www.phytozome.org/";) makeTxDbPackage(txdb = gmax189, version = "0.9.1", maintainer = "Tengfei Yin", author = "Tengfei Yin", destDir=&