GenePattern is a powerful genomic analysis platform that provides access to more than 240 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.
GenePattern Public Server: http://genepattern.broadinstitute.org/gp/
Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501 doi:10.1038/ng0506-500.
ATARiS is a computational method designed to analyze phenotypic readouts from multiple-sample RNAi screens in which each gene is targeted by multiple RNAi reagents. “ATARiS” stands for Analytic Technique for Assessment of RNAi by Similarity. ATARiS was developed by Aviad Tsherniak in the lab of Jill Mesirov.
Shao DD, Tsherniak A, Gopal S, Weir BA, Tamayo P, Stransky N, Schumacher SE, Zack TI, Beroukhim R, Garraway LA, Margolin AA, Root DE, Hahn WC, Mesirov JP. ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens. Genome Res. 2013 Apr;23(4):665-78. doi: 10.1101/gr.143586.112.
GENE-E is a matrix visualization and analysis platform designed to support visual data exploration. It includes heat map, clustering, filtering, charting, marker selection, and many other tools. In addition to supporting generic matrices, GENE-E also contains tools that are designed specifically for genomics data. GENE-E was created and is developed by Joshua Gould.
PARIS is a flexible GenePattern module which uses a mutual information based metric to rank cell line data (shRNA/gene dependencies, genomic features, chemical sensitivities, etc.) based on a classifier feature (one value per cell line). The module can handle both binary and continuous variables as the classifier feature. PARIS was developed by Pablo Tamayo.