Blog Archives

When can we expect the last damn microarray paper?

January 18, 2012
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When can we expect the last damn microarray paper?

With bonus R codeIt came as a shock to learn from PubMed that almost 900 papers were published with the word "microarray" in their titles last year alone, just 12 shy of the 2010 count. More alarming, many of these papers were not of the innocuous "Microarray study of gene expression in dog scrotal tissue" variety, but dry...

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Making R’s paste act more like CONCAT

October 31, 2011
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While vector-friendly, R's paste function has a few behaviors I don't particularly like. One is using a space as the default separator:> adjectives> paste(adjectives,"er")> paste(adjectives,"er") "lean er" "fast er" "strong er" #d'oh> paste(adjectives,"er",sep="") "leaner" "faster" "stronger"Empty vectors get an undeserved first class treatment: > paste(indelPositions,"i",sep="") "i"> indelPositions> paste(indelPositions,"i",sep="") "5i"...

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Installing RStudio Server on Scientific Linux 6: My bash notebook

August 18, 2011
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Installing RStudio Server on Scientific Linux 6: My bash notebook

Granted, not a brilliant sysadmin mind at work here, but this might help someone someday.Scientific Linux (SL) is built from Red Hat Enterprise LinuxSee installation instructions here:http://rstudio.org/download/server$ sudo rpm -Uvhhttp://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-5.noarch.rpm password for leipzig: Retrievinghttp://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-5.noarch.rpmwarning: /var/tmp/rpm-tmp.S2RQAH: Header V3 RSA/SHA256 Signature, key ID0608b895: NOKEYPreparing... ...

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RStudio: My thoughts

March 15, 2011
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RStudio: My thoughts

Let me get this out of the way: I just love RStudio.Created by a team lead by JJ Allaire, a name that should ring a bell if you were involved in web development during the Clinton administration, RStudio is an R IDE that is actually designed for R from...

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RStudio: My thoughts

March 15, 2011
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RStudio: My thoughts

Let me get this out of the way: I just love RStudio.Created by a team lead by JJ Allaire, a name that should ring a bell if you were involved in web development during the Clinton administration, RStudio is an R IDE that is actually designed for R from...

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Chromosome bias in R, my notebook

December 23, 2010
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Chromosome bias in R, my notebook

My goal is to develop a means of detecting chromosome bias from a human BAM file.Because I've been working with proprietary and novel plant genomes for the last three years, I haven't had the chance to use any of the awesome UCSC-based annotational features that have been introduced and refined in Bioconductor until now. I've returned to biomedical research...

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Chromosome bias in R, my notebook

December 23, 2010
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Chromosome bias in R, my notebook

My goal is to develop a means of detecting chromosome bias from a human BAM file.Because I've been working with proprietary and novel plant genomes for the last three years, I haven't had the chance to use any of the awesome UCSC-based annotational features that have been introduced and refined in Bioconductor until now. I've returned to biomedical research...

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Getting the basics from readAligned

March 9, 2010
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The UCR guide is a little sparse with regard to getting basic information from readAligned.I'd like to add to the general cookbook. If some bioc people out there can contribute some alignment recipes can fill me in on some more basics please comment:alignedReads #how many reads did I attempt to align#i don't think you can't get this from...

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Getting the basics from readAligned

March 9, 2010
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The UCR guide is a little sparse with regard to getting basic information from readAligned.I'd like to add to the general cookbook. If some bioc people out there can contribute some alignment recipes can fill me in on some more basics please comment:alignedReads #how many reads did I attempt to align#i don't think you can't get this from...

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Quality trimming in R using ShortRead and Biostrings

March 3, 2010
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I wrote an R function to do soft-trimming, right clipping FastQ reads based on quality.This function has the option of leaving out sequences trimmed to extinction and will do left-side fixed trimming as well.#softTrim#trim first position lower than minQuality and all subsequent positions#omit sequences that after trimming are shorter than minLength#left trim to firstBase, (1 implies no left trim)#input:...

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