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Oligo package

Implements a unified framework for preprocessing microarray data and interfaces with other BioConductor tools for downstream analysis. The Oligo package provides array coordinates, feature types, sequences, feature names and other relevant information for preprocessing. Developers can use oligo solutions to facilitate the integration of their tools with BioConductor. They also benefit from the unified model that the package makes available, as the consistency in data delivery and handling improves efficiency.

omeSOM / transcript/metabol-ome Self Organizing Map

Gives support to the data mining task applied to both basic research and applied breeding programs oriented towards discovering unknown relationships among data. *omeSOM trains a 2D Self-Organizing Map (SOM) for the analysis and interpretation of large amounts of data of different types, such as gene expression and metabolite profiling. The software also provides simple visualizations for the identification of co-expressed genes and co-accumulated metabolites.

MiCoViTo / Microarray Comparison Visualization Tool

Identifies and visualizes groups of genes that having similar expression in two sets of microarray experiments representing two distinct transcriptome states. MiCoViTo is a user-friendly tool composed of three parts: (i) a set of programs for microarray data preprocessing and for comparing expression profiles, (ii) a web-interface and, (iii) a relational database. It aims to help biologists achieve an intuitive understanding of their own data using an approach based on the comparison of sets of microarray experiments.