PINCAGE is a method that uses probabilistic integration of cancer genomics data for combined evaluation of RNA-seq gene expression and 450K array DNA methylation measurements of promoters as well as gene bodies.
RECOG is a workbench software program which is used to conduct comparative genome analyses on a massive scale. The main feature of RECOG is the function of ortholog analysis between genomes of numerous species based on the display of an ortholog table (rows: ortholog groups; columns: species).RECOG can also conduct various comparative analyses for detailed examination, based on this table.
geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available plug-ins supporting the visualization and analysis of gene expression and sequence data.
caOmicsV package provides methods to visualize multi-dimentional cancer genomics data including of patient information, gene expressions, DNA methylations, DNA copy number variations, and SNP/mutations in matrix layout or network layout.
Trebol is a multi-platform software for comparative genome analyses with functionalities such as sequence retrieving, generation of sequence comparisons, visualization, edition and rendering of high quality images for scientific publications.