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TCGAretriever (version 1.3)

Retrieve Genomic and Clinical Data from TCGA

Description

The Cancer Genome Atlas (TCGA) is a program aimed at improving our understanding of Cancer Biology. Several TCGA Datasets are available online. 'TCGAretriever' helps accessing and downloading TCGA data hosted on 'cBioPortal' via its Web Interface (see for more information). Features of 'TCGAretriever' include: 1) it is very simple to use (get all the TCGA data you need with a few lines of code); 2) performance (smooth and reliable data download via 'httr'); 3) it is tailored for downloading large volumes of data.

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Version

Install

install.packages('TCGAretriever')

Monthly Downloads

193

Version

1.3

License

GPL-2

Maintainer

Damiano Fantini

Last Published

July 30th, 2016

Functions in TCGAretriever (1.3)

get_ext_mutation

Retrieve Extended Information About DNA Mutations from TCGA

get_cancer_studies

Retrieve a List of Cancer Studies Available at TCGA

get_cancer_types

Retrieve a List of Cancer Types as Defined by the TCGA Guidelines

fetch_all_tcgadata

Recursively Fetch All Data Included in a TCGA Study Subset

get_genetic_profiles

Retrieve Genetic Profiles for a TCGA Study of Interest

get_clinical_data

Retrieve Clinical Information from a TCGA Study

get_profile_data

Retrieve TCGA Data corresponding to a Specific Genetic Profile of Interest

trim_rnaseq_tcgadata

RNAseq Expression Data Trimmer

get_protein_info

Retrieve Information on Antibodies Used for Protein Levels Determination

get_protein_data

Retrieve Protein Expression Data from a TCGA Study

TCGAretriever-package

Retrieve Genomic and Clinical Data from TCGA

Split Numeric Vectors in Groups

basic_tcga_query

TCGA Core Query Engine

Explode TCGA Case Identifiers from a TCGA Study

Retrieve All Case List Available for a Specific TCGA Study