TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources.
Luca Lenzi,Federica Facchin,Francesco Piva,Matteo Giulietti,Maria Chiara Pelleri,Flavia Frabetti,Lorenza Vitale,Raffaella Casadei,Silvia Canaider,Stefania Bortoluzzi,Alessandro Coppe,Gian Antonio Danieli,Giovanni Principato,Sergio Ferrari,Pierluigi Strippoli +14 more
TL;DR: TRAM is designed to create, and statistically analyze, quantitative transcriptome maps, based on gene expression data from multiple sources, and is able to perform intra-sample and inter-sample data normalization, including an original variant of quantile normalization (scaled quantile), useful to normalize data from platforms with highly different numbers of investigated genes.
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Abstract: Background
Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format) and they typically accept only gene lists as input.
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