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: rMAT
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 [...]
rMAT soon to support Grand Central Dispatch
In my spare time, I have been playing a bit with GCD, and the R package rMAT. My first impression is that it’s very easy to use and works as advertised. I have actually used it to parallelize the normalization processing of multiple tiling arrays. This will soon be incorporated in the R package rMAT, [...]
rMAT available from Bioconductor
We have recently released rMAT, the R version of the python software MAT. You can download the package from Bioconductor. We are still working on improving the package by adding new functionality, but the current version should already be sufficient to efficiently analyze chip-chip data. If you have any comments/suggestions about the package. Please make [...]
