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 [...]
Tag Archives: Bioinformatics
flowClust free from mclust
I just wanted to post a quick note about flowClust. As of version 2.6, flowClust does not depend on mclust anymore. So for those of you who emailed us because you wanted to use flowClust but you found the mclust license too restrictive, you are now free to use flowClust! Because flowClust is distributed under [...]
flowTrans available from Bioconductor
Greg Finak has just released a Bioconductor/R package for estimating and fitting various transformation to flow cytometry data. The package, flowTrans, has been designed to play well with flowCore and flowClust. This is just a start and we hope to improve the package in the near future, but we wanted to release it ASAP so [...]
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 [...]
Congratulations to Marie-Pier and Greg!
Congratulations to Marie-Pier Scott-Boyer and Greg Finak who have both won a prize in the poster competition at the 2009 Robert-Cedergren colloquium in Bioinformatics. Marie-Pier won the best poster in the PhD category for her work on “Modeling gene expression networks with genomic data to identify determinants of complex quantitative traits in mouse hearts” and [...]
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 [...]
MonBug symposium
Today is the monbug symposium, and I thought I would send a quick note from the IRCM where it is currently taking place. We have already seen a series of great talks and I can’t wait for the next edition. You can see on this picture, Elaine Mardis, giving the second keynote lecture of the [...]
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
