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The cancer genome atlas (TCGA) data processing software tools | Genome variation analysis

The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers…
TCGA Data Portal
Dataset

TCGA Data Portal The Cancer Genome Atlas Data Portal

Generates, analyzes, and makes available genomic sequence, expression,…

Generates, analyzes, and makes available genomic sequence, expression, methylation, and copy number variation (CNV) data on over 11,000 individuals who represent over 30 different types of cancer.…

cBioPortal
Web

cBioPortal

Provides a web resource for exploring, visualizing, and analyzing…

Provides a web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. cBioPortal reduces molecular profiling data from cancer tissues and cell lines into readily…

TCGA-assembler
Desktop

TCGA-assembler

Authorizes to retrieve, assemble and process public data from The Cancer Genome…

Authorizes to retrieve, assemble and process public data from The Cancer Genome Atlas (TCGA). TCGA-assembler is an open source software which is composed of two modules: (i) the first module earns…

TCGAbiolinks
Desktop

TCGAbiolinks

Aids in querying, downloading, analyzing and integrating The Cancer Genome…

Aids in querying, downloading, analyzing and integrating The Cancer Genome Atlas (TCGA) data. TCGAbiolinks can: i) facilitate the TCGA open-access data retrieval, ii) prepare the data using the…

TCGA2STAT
Desktop

TCGA2STAT

An open source software package to obtain the TCGA data, wrangle it, and…

An open source software package to obtain the TCGA data, wrangle it, and pre-process it into a format ready for multivariate and integrated statistical analysis in the R environment. In a…

CrossHub
Desktop

CrossHub

A software tool that integrates multi-resource omics data. CrossHub was…

A software tool that integrates multi-resource omics data. CrossHub was designed to analyze TCGA transcriptomic and epigenomic data in the context of ENCODE, Jaspar and various miRNA target…

MultiAssayExper…
Desktop

MultiAssayExperiment

Provides data structures and methods to represent, manipulate, and integrate…

Provides data structures and methods to represent, manipulate, and integrate multi-assay genomic experiments. MultiAssayExperiment permits to integrate any data class that supports basic subsetting…

MEXPRESS
Web
Desktop

MEXPRESS

Allows the integration and visualization of the expression, DNA methylation and…

Allows the integration and visualization of the expression, DNA methylation and clinical TCGA (The Cancer Genome Atlas) data on a single-gene level. MEXPRESS was designed after the principles of…

RTCGAToolbox
Desktop

RTCGAToolbox

Allows users to systematically access Firehose pre-processed data, and to…

Allows users to systematically access Firehose pre-processed data, and to organize it for easy management and analysis. The library also allows users to create data matrices from TCGA data, without…

Web-TCGA
Web

Web-TCGA

A web based, freely accessible online tool, which can also be run in a private…

A web based, freely accessible online tool, which can also be run in a private instance, for integrated analysis of molecular cancer data sets provided by TCGA. In contrast to already available…

Zodiac
Web
Desktop

Zodiac

Allows investigation of molecular interactions in cancer. Zodiac integrates…

Allows investigation of molecular interactions in cancer. Zodiac integrates big-data analysis on multimodal TCGA data and produces knowledge of molecular interactions in cancer. It is based on…

canEvolve
Web

canEvolve

Allows researchers to query results of different types of analysis with a view…

Allows researchers to query results of different types of analysis with a view to generate novel hypotheses. canEvolve stores functional genomics and other large-scale data on cancer. It assists…

TCIA
Dataset

TCIA The Cancer Imaging Archive

The image data is organized into purpose-built collections of subjects. The…

The image data is organized into purpose-built collections of subjects. The subjects typically have a cancer type and/or anatomical site (lung, brain, etc.) in common. Each link in the table below…

firehose_get
Desktop

firehose_get

Helps to simplify retrieval of data and analysis results. firehose_get permits…

Helps to simplify retrieval of data and analysis results. firehose_get permits to retrieve open-access results of Broad Institute Cancer Genome Atlas (TCGA) GDAC runs.

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