The ISA infrastructure now includes an R package, called Risa, to parse ISAtab datasets into R objects. The Risa package is included in BioConductor release 2.11.
Risa provides functionality to read ISA-Tab datasets into R objects. These objects can then be used by downstream Bioconductor packages for data analysis and visualization (i.e, xcms). Currently, metadata associated to proteomics and metabolomics-based assays (i.e. mass spectrometry) can be processed into xcmsSet objects (from the xcms Bioconductor package). Risa also provides functionality to save the ISA-tab dataset, or each of its individual files, and to update assay files after analysis. For an example of using Risa for processing and analysis of metabolomics data, see https://github.com/sneumann/mtbls2.
The source code and latest version can be found in the GitHub repository https://github.com/ISA-tools/Risa. Please, submit all ‘bugs’ and feature requests through https://github.com/ISA-tools/Risa/issues.