Last update: 17/07/2003

Here are things I am using, have been using, or just toyed with that you may consider looking at...

Homemade

bioinformatics
3D visualization of oligonucleotide array data from a well known manufacturer (only for Affymetrix CEL and CDF files for the moment, if anybody is interested in seeing a particular format being implemented just contact me). The program was developped and tested under Linux using the jdk and the java3d implementation from blackdown. It ran under Windows 98 (JRE from Sun, DirectX Java3d version).. Once you run it, loaded a data and opened the 3D window, try to move the mouse up while holding the middle mouse button pressed. Download the version 0.2a. (knowing this is still primitive, looking fancy, and that you may have to figure out the use for it).
affyR	An R package to analyze Affymetrix data. I have been developping it (and using it) for about 3 months now. It should be fairly stable, decently complete (yet not comprehensive) and expandable. A poster about it has been accepted and will be presented early february... The package has been absorbed by the bioconductor project... SEE BELOW
affy	A R package to analyze Affymetrix data, developped with Rafael Irizarry download the manual (work in progress) (to download the package the best place is bioconductor).
splicegear	A R package to handle alternative splicing data, and combine them with other data (especially expression data)
affypdnn	A R package to extend the package 'affy' with the PDNN method

From elsewhere

statistics / data analysis
R	A language for data analysis and statistics (sometimes referred to as the GNU 'S') (tips for R) (searchable r-help list)
bioinformatics
Rexpress	An excellent up-to-date list of R-packages related to microarrays by Korbinian Strimmer. A sure place to be on the cutting edge.
J-Express	Expression analysis software, free for academics / non-profit use.
MICE	A Molecular Interactive Collaborative Environment.
XGobi	Data visualization