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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

  • Broad-Novartis Cancer Cell Line Encyclopedia (CCLE)

    The Cancer Cell Line Encyclopedia (CCLE) project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access analysis and visualization of DNA copy number, mRNA expression and mutation data for about 1000 cell lines. 

  • Cancer Portals

    A number of cancer portals have been developed to streamline viewing and analysis of related data.

  • ChemBank

    ChemBank is the flagship project of the Chemical Biology Program and Platform, incorporating small-molecule structure and screening data from the Broad Institute's high-throughput screening facilities.

  • Differentiation Map Portal (DMAP)

    The Differentiation Map Portal (DMAP) contains data and publications used in the study of a differentiation map of hematopoiesis.

  • 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.

  • Integrative Genomics Portal (IGP)

    The Broad Integrative Genomics Portal allows the sharing (both private and public) of annotated and integrated genomic datasets. Funded by the Starr consortium, the portal provides both data analyses and visualizations.

  • Multiple Myeloma Genomics Portal (MMGP)

    The Multiple Myeloma Genomics Portal (MMGP) provides access to and analysis of the MMGP portal data sets. These include the MMRC-funded reference collection of paired aCGH and gene expression data as well as several additional public multiple myeloma datasets.

  • Tumorscape

    The Tumorscape portal facilitates the use and understanding of high resolution copy number data amassed from multiple cancer types. It supports gene-level analysis, analysis by cancer type, and the downloading/browsing of data.