User: heyi xiao

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heyi xiao360
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360
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United States
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2 years, 6 months ago
Joined:
10 years, 1 month ago
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Posts by heyi xiao

<prev • 38 results • page 1 of 4 • next >
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Comment: C: can KEGG figures produced by pathview be used in publication, or that they are c
... KEGG website says that academic users may freely use them: http://www.kegg.jp/kegg/legal.html. If you have any concern you may contact KEGG directly. ...
written 2.6 years ago by heyi xiao360
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IRanges installation problem
... I tried to install IRanges package using biocLite() on my linux box, I got the following error: … Error in setGeneric(f, where = where) :   'anyNA' is a primitive function;  methods can be defined, but the generic function is implicit, and cannot be changed. Error : unable to load R code in pack ...
iranges written 4.3 years ago by heyi xiao360
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ENCODE integrated genomic annotation data access
... I try to use ENCODE annotation data in my own data analysis. I couldn’t find a introductory tutorial on ENCODE data access and usage. So I explored a little on myself. I found that the old data of ENCODE production phase (2007-2012) can be viewed and accessed from UCSC: http://genome.ucsc.edu/ENCOD ...
annotation written 4.5 years ago by heyi xiao360
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Problems with per package download statistics
... I notice that the per package download statistics pages are down for many (but not all) packages for quite a while. For instance, the few p letter packages: the first and second one have problems, but the third one is okay. http://bioconductor.org/packages/stats/bioc/parody.html http://bioconductor. ...
written 5.2 years ago by heyi xiao360
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Answer: A: Problems with per package download statistics
... I notice that the per package download statistics pages are down for many (but not all) packages for quite a while. For instance, the few p letter packages: the first and second one have problems, but the third one is okay. http://bioconductor.org/packages/stats/bioc/parody.html http://bioconductor. ...
written 5.2 years ago by heyi xiao360
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Comment: C: VariantTools callVariants - binomial likelihood ratio
... Hi Michael, Thanks for your answers. Now I understand the lrtFreqCutoff step. I think the the values of p0 (=perror = 0.001) and p1 (=plower = 0.2) should be important for snp calling. Sequencing error, p0/perror, can be derived from the raw read data, or even better can be recalibrated like SOAPsnp ...
written 5.4 years ago by heyi xiao360
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VariantTools callVariants - binomial likelihood ratio
... Hi, I try to use VariantTools package package and I am working on the vignette examples. I have some questions on the variant calling procedure. The vignette says: ?The callVariants function uses a binomial likelihood ratio test for this purpose. The ratio is P(D|p = plower)=P(D|p = perror).? To un ...
varianttools written 5.4 years ago by heyi xiao360 • updated 5.4 years ago by Michael Lawrence10k
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Comment: C: VariantTools: callVariants error
... Okay, I reinstalled/updated VariantAnnotation and BiocParallel using biocLite(). Only after restart a new R session, callVariants works now. I appreciate Herv??s suggestion too, I will update all other packages when I get time. -------------------------------------------- On Wed, 11/13/13, Hervé Pa ...
written 5.4 years ago by heyi xiao360
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VariantTools: callVariants error
... I tried the Basic usage example in VariantTools. I got error at the callVariants step. The error message shows that the indirect call to BiocParallel::bpmapply had some problem, but not sure what that is. Note that my VariantTools and depends are up-to-date. Below is the error and sessionInfo(). Tha ...
varianttools written 5.4 years ago by heyi xiao360 • updated 5.4 years ago by Michael Lawrence10k
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Comment: C: VariantTools installation problem: dependencies not available
... Thanks Michael, for all the info! -------------------------------------------- On Tue, 11/12/13, Michael Lawrence wrote: Subject: Re: [BioC] VariantTools installation problem: dependencies not available Cc: "Michael Lawrence" , "Martin Morgan" , "bioconductor at r-project.org" Date: Tuesday, ...
written 5.4 years ago by heyi xiao360

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