Articles by Jeremy Leipzig

When can we expect the last damn microarray paper?

January 18, 2012 | Jeremy Leipzig

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 ... [Read more...]

Making R’s paste act more like CONCAT

October 31, 2011 | Jeremy Leipzig

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")[1] "lean er" "fast er" "strong er" #d'oh__ paste(adjectives,"er",sep="")[1] "leaner" "faster" "stronger"Empty vectors get an undeserved first class ... [Read more...]

Installing RStudio Server on Scientific Linux 6: My bash notebook

August 18, 2011 | Jeremy Leipzig

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:[leipzig@localhost ~]$ sudo rpm -Uvh[sudo] password ... [Read more...]

RStudio: My thoughts

March 15, 2011 | Jeremy Leipzig

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...
[Read more...]

Chromosome bias in R, my notebook

December 23, 2010 | Jeremy Leipzig

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 ... [Read more...]

Getting the basics from readAligned

March 9, 2010 | Jeremy Leipzig

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 ... [Read more...]

Quality trimming in R using ShortRead and Biostrings

March 3, 2010 | Jeremy Leipzig

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 ... [Read more...]

R’s xtabs for total weighted read coverage

November 4, 2009 | Jeremy Leipzig

Samtools and its BioPerl wrapper Bio::DB:Sam prefer to give read coverage on a depth per base pair basis. This is typically an array of depths, one for every position that has at least one read aligned. OK, works for me. But how can we quickly see which targets (... [Read more...]

Standardized Velvet Assembly Report

August 25, 2009 | Jeremy Leipzig finally got my Velvet Assembler report script up on google code. This "program" consists of some short scripts and a Sweave report designed to help Velvet users identify the optimal kmer an... [Read more...]

Calculating an N50 from Velvet output

November 25, 2008 | Jeremy Leipzig

In sequencing circles the N50 length is a useful heuristic for judging the quality of an assembly. Here is my definition of N50 length, which you may or may not find intuitive: N50 length is the length of the shortest contig such that the sum of contigs of equal length ... [Read more...]

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