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TCGAretriever (version 1.5)

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). 'TCGAretriever' is easy to use (get all the TCGA data you need with a few lines of code), enforces reliable data download (via 'httr'), and is suitable for downloading large volumes of data.

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Version

Install

install.packages('TCGAretriever')

Monthly Downloads

193

Version

1.5

License

GPL-2

Maintainer

Damiano Fantini

Last Published

December 17th, 2019

Functions in TCGAretriever (1.5)

basic_tcga_query

TCGA Core Query Engine
make_groups

Split Numeric Vectors in Groups
get_protein_info

Retrieve Information on Antibodies Used for Protein Levels Determination
get_protein_data

Retrieve Protein Expression Data from a TCGA Study
get_profile_data

Retrieve TCGA Data corresponding to a Specific Genetic Profile of Interest
get_case_lists

Retrieve All Case List Available for a Specific TCGA Study
get_clinical_data

Retrieve Clinical Information from a TCGA Study
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
get_ext_mutation

Retrieve Extended Information About DNA Mutations from TCGA
get_genetic_profiles

Retrieve Genetic Profiles for a TCGA Study of Interest
TCGAretriever-package

Retrieve Genomic and Clinical Data from cBioPortal
expand_cases

Explode TCGA Case Identifiers from a TCGA Study
fetch_all_tcgadata

Recursively Fetch All Data Included in a TCGA Study Subset