Last month’s issue of The Scientist had an interesting article about flow cytometry data analysis, and in particular about software and tools available for data analysis. The good news is that the article mention Bioconductor. The bad news is that it was almost a simple footnote, to quote the article it said: “Don’t forget freeware. [...]
Archive | Software RSS feed for this section
rMAT and openMP
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 [...]
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 [...]
rGADEM soon to support Grand Central Dispatch
So I just wanted to post an update regarding our development of rGADEM. As I said in a previous post, we have been working very hard to improve the computing efficiency of our ChIP-seq pipeline. After PICS, that supports parallel computing via snowfall, rGADEM will soon support Grand Central Dispatch (GCD) on Snow Leopard. As [...]
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 [...]
flow cytometry special issue
Some of the papers to be published as part of the special issue on bioinformatics approaches to flow cytometry have started to appear online. I expect that all papers accepted will be available soon, including our own paper on flowMerge. If you have not looked at flowMerge yet, please try the R package available from [...]
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, [...]
Grand Central Dispatch
A few days ago I finally upgraded to Snow Leopard. I was writing a few grants, so I did not want to take the chance to upgrade before submitting these grant applications. Anyway, I am now running Snow Leopard, and even though there are no “new” apparent features, it is a great upgrade. In my [...]
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.
