Analytical Tools

The Cancer Imaging Archive (TCIA) - A service providing 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. (National Cancer Institute)

The Cancer Proteome Atlas (TCPA) - An integrative data portal for accessing, visualizing, and analyzing proteomic data. (MD Anderson Cancer Center)

cBioPortal for Cancer Genomics - Provides visualization, analysis, and download of large-scale cancer genomics data sets. (Memorial Sloan-Kettering Cancer Center)

Copy Number Portal - A portal for exploring copy number alterations of TCGA data, including results of GISTIC analyses for identifying genes targeted by somatic copy number alterations that drive cancer growth. (Broad Institute)

DeMixT - A software package thatdeconvolutes transcriptome data from a mixture of two (tumor, stroma) or three components (tumor, stroma, immune). It provides both the mixture proportions and individual sample-specific and gene-specific expression levels for each component. (MD Anderson Cancer Center)

FASMIC - An integrative, analytic web platform for annotating the functional impacts of somatic mutations in human cancer. (MD Anderson Cancer Center)

Firehose - A suite of methods and pipelines developed for processing and analyzing various types of large-scale genomic and proteomic data. (Broad Institute) 

Firebrowse - A web portal to explore and visualize cancer data generated by Broad GDAC Firehose. Provides graphical tools like viewGene to explore expression levels and iCoMutto explore a comprehensive mutation analysis of each TCGA disease and an API for programmers. (Broad Institute)

FunSeq2 - A tool to prioritize and annotate somatic variants, particularly non-coding variants, from cancer whole genome sequencing. Uses a pre-built data context generated from multiple genomic and cancer resources that is regularly updated. (Weill Cornell Medicine)

Integrative Genomics Viewer (IGV) - A high-performance visualization tool for interactive exploration of large, integrated data sets. (Broad Institute)

MBatch - A web-based tool for identifying and quantifying batch effects present in processed TCGA data, utilizing hierarchical clustering and enhanced PCA plots. (MD Anderson Cancer Center)

Morphometric Data - A service that allows the TCGA community to download computed histology-based information and visualize images overlaid with computed information. (Lawrence Berkeley National Laboratory)

Mutation calling using a Markov Substitution model for Evolution (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. (MD Anderson Cancer Center and Baylor College of Medicine)

Regulome Explorer - Web-based interactive tools for visualizing and exploring associations between clinical and molecular TCGA data. (Center for Systems Analysis of the Cancer Regulome) 

SurvNet - A web-based tool for identifying network-based biomarkers that correlate with patient survival data. (MD Anderson Cancer Center)

TANRIC - An integrative web server for exploring the functions of lncRNAs in cancer. (MD Anderson Cancer Center)

TumorMap - An interactive portal for visualizing high-dimensional omics data in a 2-dimensional projection rendered with the Google Maps API. A toolbox of statistical tests allows researchers to find associations between sample groupings and clinical, phenotypic, and molecular event annotations. (UC Santa Cruz)

Xena - A suite of web-based tools to visualize, integrate, and analyze cancer genomics and its associated clinical data. (UCSC Santa Cruz)