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Software

Scientists in the Broad community have developed many critical software tools for the analysis of increasingly large genome-related datasets, and they make these tools openly available to the scientific community. For the conditions governing the use of Broad Institute software, please see the software use agreement associated with the tools you choose to download.

Use our search function, browse the complete software collection or click on one of the software categories listed below:

All   Chemical Biology     Image Analysis     Proteomics     Portals     Tool Suites    Visualization
Genetic Analysis:   GWAS   Genetic Variation   Linkage Analysis   Gene Expression
Sequence Analysis:   Assembly   Annotation   Alignment   RNAi   RNA-seq   Primer Design   Next Generation Tools   Phylogenetic Analysis   Gene Structure  Viral

  • GENE-E

    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 RNAi and gene expression data.

  • GenePattern

    GenePattern is a powerful genomic analysis platform that provides access to more than 150 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..

  • ICBP Data & Analysis Portal

    The ICBP Data and Analysis Portal serves as an information hub of the ICBP program enabling resource sharing, annotation, and data integration and analysis. The portal provides access to datasets, analysis tools, visualizations, and other resources produced by the ICBP Centers for Cancer Systems Biology.