RNA-robin: identification of expressed mutational cancer driver genes.

facopy (bioconductor.org/packages/bioc/html/facopy.html): feature-based association and gene-set enrichment for copy number alteration analysis in cancer.

seqCNA (bioconductor.org/packages/bioc/html/seqCNA.html): copy number analysis of high-throughput sequencing cancer data with integrated summarization, extensive filtering and improved normalization.

CnaStruct (web.bioinformatics.cicbiogune.es/cnastruct): bivariate segmentation of SNP array data for allele-specific copy number analysis in R.

CnaGen (web.bioinformatics.cicbiogune.es/cnagen): generation of synthetic data to emulate tumour samples on SNP arrays in R.

TilAnalyze (tiling.mosen.es): extensible and user-friendly Java software for the analysis of tiling microarrays.

Nubia (nubia.mosen.es): Java-based framework for the integration of context-aware autonomous systems.