ABSTRACT
The Bioconductor project (www.bioconductor.org) is a software and documentation repository for components useful in workflows for the analysis of genome-scale data. All the software provided through Bioconductor is coded so that it can be used with the R language (www.r-project.org). Thus, the majority of source code for Bioconductor is actually written in R, but, thanks to the emphasis accorded to interoperability in the R project, algorithms coded in C, C++, Java, and other languages are also present. The basic requirements for software contributions in the Bioconductor project are
ˆ code is delivered in the form of an R package – a formally specified set of folders with reserved names including checkable documentation and configuration files;
cluded, that illustrates use of the software in an analysis process – this is distinct from the software manual pages, also required, that provide details on the calling sequences and behaviors of specific routines;
ˆ the code must pass a formal checking process for the current version of R, which is revised approximately every six months;
ˆ the code must be formally licensed using a license compatible with open source distribution – base Bioconductor packages use Artistic 2.0 at this time.
