User: km

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km100
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Posts by km

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Rgraphviz installation issue
... I am using gcc 4.7.3 on ubuntu Linux 13.04 ( x86_64 arch). Here is the complete trace: R version 3.0.1 (2013-05-16) -- "Good Sport" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. Y ...
written 4.0 years ago by km100
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Rgraphviz installation issue
... Hi all, I am unable to install Rgraphviz as a dependency for gage package. I am using R (3.0.2) and bioconductor 2.13. > biocLite('Rgraphviz') BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. Installing package(s) 'Rgraphviz' trying ...
rgraphviz gage written 4.0 years ago by km100 • updated 4.0 years ago by Luo Weijun1.4k
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topgo GO mapping for non model organisms
... Hi all, I am planning to use topgo for GO enrichment of RNA-seq data from tophat/cufflinks pipeline. I have a non-model organism and hence donot have GO mappings in bioconductor annotation package. How do I obtain the GO mappings for my organism genes (universe) and how do I plug it into the topgo ...
annotation go organism topgo written 4.3 years ago by km100
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Pathview published in Bioinformatics
... Dear All, Is this package useful to do pathway analysis with RNA-seq based expression data - say for eg. gene expression analysis results from tophat/cuflinks pipeline ? Regards, Krishna Mohan On Fri, Jun 28, 2013 at 4:19 AM, Luo Weijun wrote: > > > A little more info. You > may ...
visualization graph pathview written 4.4 years ago by km100
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custom SNPlocs / BSgenome package
... Hi, On Mon, Nov 28, 2011 at 8:00 AM, Valerie Obenchain wrote: > Hi kmo, > > For the BSgenome, you can follow the "How to forge a BSgenome data > package" document, > > http://bioconductor.org/**packages/2.10/bioc/html/**BSgenome.html > > I'm not sure what you mean by "a ...
snp annotation organism homo sapiens bsgenome snplocs written 6.0 years ago by km100 • updated 6.0 years ago by Hervé Pagès ♦♦ 13k
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custom SNPlocs / BSgenome package
... Hi all, How do I make a custom BSGenome package for a given genome and SNPlocs package for it ? I appreciate any pointers. Thanks, Regards, kmo [[alternative HTML version deleted]] ...
bsgenome written 6.0 years ago by km100 • updated 6.0 years ago by Valerie Obenchain ♦♦ 6.4k
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unique human genomic regions
... I'm trying to look if are there any regions unique to human genome and that are not found in mouse genome. could you pls suggest bioc packages that would help me ? [[alternative HTML version deleted]] ...
written 6.2 years ago by km100
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Answer: A: NGS service providers
... Hi, you could check with genotypic.co.in for competitive pricing. KM On Tue, Jul 5, 2011 at 2:39 PM, Noemi Andor wrote: > Dear BioC list, > > I am looking for a NGS service preferentially located in US, California but > alternatively also in germany. The project I'm working on invo ...
written 6.4 years ago by km100
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Comment: C: Group millions of the same DNA sequences?
... you could try CD-HIT. http://bioinformatics.ljcrf.edu/cd-hi/ meant to work with huge number of sequences. regards KM On Thu, Nov 18, 2010 at 2:53 PM, Stijn van Dongen wrote: > > On Thu, Nov 18, 2010 at 09:21:07AM +0800, Xiaohui Wu wrote: >> Thank you Aaron! ?Till now, sort and uniq m ...
written 7.1 years ago by km100
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biocLite() partial install of pakcages issue
... Hi all, I notice that when I install bioconductor, biocLite() call fails to fetch some packages. But it installs some packages at the end of the installation. Now if I run biocLite() again, I expect it to skip installed pakages and retry fetching those packages not installed. Surprisingly, biocLi ...
process written 7.1 years ago by km100 • updated 7.1 years ago by Martin Morgan ♦♦ 21k

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