Blue Collar Bioinformatics
Just wanted to recommend Blue Collar Bioinformatics a slick blog with lots of useful bioinformatics scripts. Everything is written in python and the full working source is typically available on GIT.
F$@%ing R: Adventures with Tcltk in OSX
I've got a bunch of RNA-seq reads I need to analyze and for the the most part I've been writing my own code to do the analysis. However, a recent paper in BioInformatics (Wang et al. 2009) describes a new R package for the identification of differentially expressed genes in RNA-seq datasets. R is a pretty straightforward language with a built-in installation system so I should just have to type two lines of code...
source("http://bioconductor.org/biocLite.R")
biocLite("DEGseq")
Not so quick. When I ran this code R tells me it can't find the DEGseq library. A bit more poking around on the internets and I discover that there's an alternate download site:
source("http://bioinfo.au.tsinghua.edu.cn/software/degseq/DEGseqInstall.R")
But after installing some dependancies it also spits out a bunch of errors. I compare the errors... Hmmm... Both installs appear to by dying on the tcl/tk install, but tcltk is a default R library. I can see it right there in "/Library/Frameworks/R.framework/Resources/library". Two hours later and after trying a bunch of crap I find this helpful website:
http://cran.r-project.org/bin/macosx/tools/
A quick and dirty install of the tcltk-8.5.5-x11.dmg and now "library(tcltk") works like a charm. No errors.
I install DEGseq with the following set of commands:
source("http://bioconductor.org/biocLite.R")
biocLite("DEGseq")
Now, a day an a half later I can see if it's useful. Woo.
Citations:
L Wang, Z Feng, X Wang, X Wang, X Zhang. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics (2009)
PYTHON Quick Links
I write a lot of code using the PYTHON Programing Language. I just gave a very brief overview to a friend who has to learn it this summer. In the course of this lesson, it occurred to me that a lot of the bioinformatic resources that I use every day are not collected in one place. So I've listed a couple of the most useful modules/packages below:
- BioPython
- This package lets you interface with NCBI, parse datafiles (e.g. fastas, Genbank, blast output etc.), run blast queries, run clustalw, etc.
- SciPy
- N-dimensional array manipulation
- MatPlotLib
- Graphing.
- Python DB API
- Database integration
- Google App Engine
- Free webhosting of python cgi scripts. It's in beta.
- Django
- Python Web Application Development package. It can be used in conjunction with Google App Engine.
Here are a few addition sites that I find useful:
- Python 2.5 Quick Reference
- both html and PDF versions are available for free!
- TextMate
- OS X text editor. It's not free, but there is a student discount available
- Forklift
- OS X ftp program. Also not free, but reasonably priced.
OOE: Another blog I help write
- From Tophat to Pysam July 21, 2010I recently needed to interact with a SAM file in python that was created as part of a Tophat run. Rather rolling my own parser I decided to use the handy pysam module. However, I immediately ran into trouble. I couldn’t get pysam to open my file. It turns out pysam requires a BAM file not a SAM file. This meant I need to convert filetypes. So, I fired up sa […]
- Inferring Heterozygosity from SNP data April 20, 2010This looks straightforward. n = total number of reads aligning to a base y = total number of reads aligning to a base that match the reference p = probability that reads match the reference base Bases with LOD>3 were called SNPs or sites of heterozygosity. From Bloom et al. (2009) Measuring differential gene expression by short read sequencing: quantitat […]
- Why we are "Python Fanboys" April 15, 2010I think I can safely say that we’re all Python evangelists. In fact, I’m pretty sure my first conversation with ‘FixedByDrift’ revolved around just how enamored with Python he is. Likewise my first email with ‘AmbiguousBase’ was a code exchange of microsatellite finding software written in Python. We just love Python. So why should you learn to love Python […]
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