BioConductor
Bioconductor is
"an open source and open development software project for the analysis and comprehension of genomic data...Bioconductor is primarily based on the R programming language but we do accept contributions in any programming language. There are two releases of Bioconductor every year (they appear shortly after the corresponding R release). At any one time there is a release version, which corresponds to the released version of R, and a development version, which corresponds to the development version of R. Most users will find the release version appropriate for their needs. In addition there are a large number of meta-data packages available. They are mainly, but not solely oriented towards different types of microarrays...Although initial efforts focused primarily on DNA microarray data analysis, many of the software tools are general and can be used broadly for the analysis of genomic data, such as SAGE, sequence, or SNP data."