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The Cancer Genome Atlas (TCGA) Computational Tools

TCGA catalyzed considerable growth and advancement in the computational biology field by supporting the development of high-throughput genomic characterization technologies, generating a massive quantity of data, and fielding teams of researchers to analyze the data.

Computational tools developed by TCGA network researchers and collaborators that were used to analyze TCGA data are available to the research community. 

TCGA Computational Tools

  • The Cancer Imaging Archive (TCIA)

    A service which de-identifies and hosts a large archive of medical images of cancer accessible for public download.

  • The Cancer Proteome Atlas (TCPA)

    A comprehensive resource for accessing, visualizing, and analyzing cancer functional proteomics.

  • cBioPortal for Cancer Genomics

    A resource that transforms multimodal data into interactive visualizations that facilitate biological discovery and clinical decision-making.

  • TCGA Copy Number Portal

    Designed to facilitate the use and understanding of high resolution copy number data amassed from cancer samples in the TCGA.

  • DeMixT

    A software package that deconvolutes transcriptome data from a mixture of two (tumor, stroma) or three components (tumor, stroma, immune).

  • FASMIC

    An integrative, analytic web platform for annotating the functional impacts of somatic mutations in human cancer.

  • Firehose

    A suite of tools and pipelines developed for processing and analyzing various types of large-scale genomic and proteomic data.

  • Firebrowse

    A tool to explore and visualize cancer data generated by Firehose.

  • FunSeq2

    A tool to prioritize and annotate somatic variants from cancer whole genome sequencing.

  • Integrative Genomics Viewer (IGV)

    A high-performance, easy-to-use, interactive tool for the visual exploration of genomic data.

  • TCGA Batch Effects Viewer

    A website designed to help assess, diagnose and correct for any batch effects in TCGA data.

  • MuSE

    A mutation caller that models the evolution of the reference allele to the allelic composition of the tumor and normal tissue at each genomic locus and accounts for tumor heterogeneity through a sample-specific error model.

  • SurvNet

    A web-based tool for identifying network-based biomarkers that correlate with patient survival data.

  • The Atlas of non-coding RNA in Cancer (TANRIC)

    An integrative web server for analyzing long non-coding RNAs (lncRNAs) in cancer.

  • Tumor Map

    An interactive browser that allows biologists, who may not have computational expertise, to richly explore the results of high-throughput cancer genomics experiments on thousands of patient samples.

  • UCSC Xena

    An online exploration tool for public and private, multi-omic and clinical/phenotype data.

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