Analytical Tools
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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.
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Cancer Genome Workbench (CGWB)
The Cancer Genome Workbench (CGWB) is an application developed by NCI that provides whole-genome and heatmap views of sample-level data.
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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 datasets.
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cBio Cancer Genomics Portal
The cBioCancer Genomics Portal 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.
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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.
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Biosig
Biosig, sponsored by the Lawrence Berkeley National Laboratory, allows the TCGA community to download computed histology-based information, and visualize images and overlaid computed information.
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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, and genome and computational scientists to easily incorporate TCGA into the backdrop of ongoing research.
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MD Anderson GDAC MBatch
The MD Anderson GDAC's TCGA Batch Effects (also known as MD Anderson GDAC MBatch or 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.
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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.
