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Analytical Tools

  • The Cancer Imaging Archive (TCIA)

    The Cancer Imaging Archive (TCIA) is a service provided by NCI that provides access to radiological imaging data sets in DICOM format from TCGA cases. TCIA supports imaging phenotype-genotype research, in addition to other imaging data sets for cancer imaging analysis.

  • Cancer Genome Workbench (CGWB)

    The Cancer Genome Workbench (CGWB) is an application developed by NCI that provides whole-genome and heat map views of sample-level data.

  • Integrative Genomics Viewer (IGV)

    The Integrative Genomics Viewer (IGV) is a high-performance visualization tool created by the Broad Institute for interactive exploration of large, integrated data sets.

  • cBioPortal for Cancer Genomics

    The cBioPortal for Cancer Genomics provides visualization, analysis, and download of large-scale cancer genomics data sets. The portal is developed and maintained by the Computational Biology (cBio) Center at Memorial Sloan-Kettering Cancer Center.

  • UCSC Cancer Genomics Browser

    The Cancer Genomics Browser is a suite of web-based tools to visualize, integrate, and analyze cancer genomics and its associated clinical data. It is developed and maintained by the UCSC Cancer Genomics Group.

  • Berkeley Morphometric Visualization and Quantification from H&E sections

    Berkeley Morphometric Visualization and Quantification from H&E sections, sponsored by the Lawrence Berkeley National Laboratory, allows the TCGA community to download computed histology-based information, and visualize images and overlaid computed information.

  • Broad GDAC Firehose

    The Broad GDAC Firehose provides L3 data and L4 analyses packaged in a form amenable to immediate algorithmic analysis. This enables a wide range of cancer biologists, clinical investigators, as well as genome and computational scientists to easily incorporate TCGA into the backdrop of ongoing research.

  • Broad Institute GDAC Firebrowse

    FireBrowse is a tool to explore cancer data, sitting on top of the Broad GDAC Firehose (see above) and backed by a powerful computational infrastructure, application programming interface (API), and online reports. Using FireBrowse, researchers can easily find any of thousands of data archives generated by Firehose. For programmers a powerful RESTful API is provided, with bindings to the UNIX command line, Python and R. For scientists, graphical tools like viewGene to explore expression levels and iCoMut are provided to explore the comprehensive analysis profile of each TCGA disease study within a single, interactive figure.

  • MD Anderson GDAC MBatch

    The MD Anderson GDAC's MBatch website enables researchers to identify and quantify batch effects present in TCGA level 3 data, currently in terms of hierarchical clustering and enhanced PCA plots. Additional tools are to be added in coming months.

  • Regulome Explorer

    Regulome Explorer facilitates the integrative exploration of associations in clinical and molecular TCGA data. Regulome Explorer is an effort by the Center for Systems Analysis of the Cancer Regulome (CSACR), a collaboration between the Institute for Systems Biology and The University of Texas MD Anderson Cancer Center. CSACR is a Genome Data Analysis Center within The Cancer Genome Atlas project.

  • Cancer Slide Digital Archive

    The Cancer Digital Slide Archive (CDSA) is a browser-based, interactive tool for viewing and annotating (in beta) TCGA diagnostic and tissue slide images. Pathology reports, clinical metadata, as well as genomics information can also be retrieved. The CSDA is being developed and maintained by the Department of Biomedical Informatics and the Winship Cancer Institute, Emory University.