User: ioannis.vardaxis

Reputation:
10
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New User
Location:
Norway/Trondheim/NTNU
Last seen:
1 month, 2 weeks ago
Joined:
1 year, 2 months ago
Email:
i***************@ntnu.no

Posts by ioannis.vardaxis

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Reading fastq file after narrowing sequences
... I solved it. I also had to narrow the qualities slot in the fastq file before saving. Now it uploads just fine. ...
written 8 weeks ago by ioannis.vardaxis10
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Reading fastq file after narrowing sequences
... Hi, I have a fastq file named fastq1 which I upload in R using: StreamFastq1=ShortRead::FastqStreamer(con=fastq1,n=2000000) fastq1yield=ShortRead::yield(StreamFastq1)   I then use the narrow funstion to narrow the reads of fastq1yield:  fastq1yield_narrowed@sread=Biostrings::narrow(fastq1yield ...
shortread fastqstreamer written 8 weeks ago by ioannis.vardaxis10
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Merge two BAM files into one paired-end file
... Hi,   I was wondering if it is possible to merge two separate BAM files into one paired-end BAM using packages from bioconductor. I know how to do it using external algorithms, but I am writing a package and I need to do it with bioconductor packages. I have two separate BAM files were pair info ...
bam file paired-end reads written 8 weeks ago by ioannis.vardaxis10
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Problem with BiocParallel::bpiterate
... Hey, I am trying to read a paired-end BAM file in chunks using BiocParallel::bpiterate but the iterations never stop, here is what I do:   bamfile=Rsamtools::BamFile(file="myBamFile",index="myBamFile",asMates=TRUE,yieldSize=1000000) snow <- BiocParallel::SnowParam(workers = 4, type = "SOCK") ...
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Comment: C: BiocParallel exporting function?
... Yes for .parallel=TRUE. I have changed the code now to bplapply, the problem is that when I read the instructions for using bplapply, bioconductor states that the BPPARAM argument should be given by the user. So this is where one has to specify which functions to export if I am not wrong. But there ...
written 14 months ago by ioannis.vardaxis10
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BiocParallel exporting function?
... Hi,   I am trying to replace doMC package with BiocParallel and I have some questions:   1: Is there a way of registering a backhead and then use plyr package with parallel=TRUE? I have tried everything but it does not seem to work, then I changed dlply etc with bplapply and everything works, ho ...
biocparallel written 14 months ago by ioannis.vardaxis10
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Question about sumbition process and biocviews
... Hi, When I upload my package to Github does the evaluation process start immediately? Or do I have to ask for it? Furthermore, during the evaluation process do I get feedback about the dependencies of my package etc? I have those in my description file, but maybe they should be placed a little dif ...
biocviews biocparallel github package submission written 14 months ago by ioannis.vardaxis10 • updated 14 months ago by Martin Morgan ♦♦ 21k
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Comment: C: BiocStyle header specification
... Ok thanks. One last question, i try to add email etc in yaml but it doesn't appear on the pdf: --- title: "pkg" author: "author" email: email@.. date: "`r doc_date()`" package: "`r BiocStyle::pkg_ver('pkg')`" output: BiocStyle::pdf_document2 vignette: > %\VignetteIndexEntry{pkg} %\VignetteE ...
written 14 months ago by ioannis.vardaxis10
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Comment: C: BiocStyle header specification
... hi, thanks for the answer. I know, but if I dont do that then i cannot use :\bioctitle[pkg]{long pkg name} and the package will only have a sort name actually i cannot use any of the biocstyle options in the yalm since biocstyle has to be loaded after the yalm. Therefore everythink is doubled. ...
written 14 months ago by ioannis.vardaxis10
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BiocStyle header specification
... Hi, I am trying to use BiocStyle to create vignette in R markdown. I read the instructions but i dont get the results i want so I was wondering what I have done wrong. I dont understand where I should place the first chuck which loads latex2. If i do it this way i get two pages with double author e ...
biocstyle written 14 months ago by ioannis.vardaxis10 • updated 14 months ago by James W. MacDonald45k

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