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MeV / Multiple experiment Viewer
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Allows to analyse, visualise and stratify large genomic data. MeV is a cloud-based application that gives access to genomic analysis tools, large public domain data sets, intuitive user interfaces, data visualization, and tools for reproducible research. The software allows user to explore the large public data sets, develop and test hypotheses and extend those explorations to their own data. It was designed for use in a variety of different scenarios.
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.
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