So we have been working on enabling openMP for rMAT. So far we have only been using Grand Central Dispatch for parallel computation as we mainly use Mac OS X 10.6. This has been available in rMAT and rGADEM for quite a bit already, and it works great. This being said, we know that not [...]
Tag Archives: R
chip-chip and chip-seq course at CSHL
I recently gave two lectures on chip-chip and chip-seq at the Cold Spring Harbor Labs as part of the “Integrative Statistical Analysis of Genome Scale Data” course. During my lectures and labs I have covered various aspects of the analysis of chip data going from raw data to enriched regions and de novo motifs. In [...]
GSL and 64 bit windows
Good news for 64-bit Windows users! Thanks to Arnaud Droit (and to Brian Ripley and Uwe Ligges who provided essential information to help solving this issue), a 64-bit version of the GSL (GNU Scientific Library) is now available on our wiki. You will find binaries for 32 and 64 bit windows as well as instruction to build [...]
ChIP-Seq pipeline: PICS, rGADEM, MotIV
I thought I would post an update about the status of our ChIP-Seq pipeline, including PICS, rGADEM and MotIV. I know we have promised to release PICS long ago, but we haven’t delivered yet. Well, things have changed today. It is now available on Bioconductor! You can get a copy here. Of course, it is [...]
flowMerge
A new package for improving automated gating of flow cytometry data is now available in BioConductor development release 2.5. flowMerge improves identification of complex cell subpopulations in flowClust models by allowing multiple components to represent the same cell subpopulation. Version 0.3.5 is now in the public repository.
R Journal
The first issue of The R Journal is now available: http://journal.r-project.org
R in the NY Times
Data Analysts captivated by the Power of R http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html
