TCGAretriever: Retrieve Genomic and Clinical Data from TCGA

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 <http://www.cbioportal.org/web_api.jsp> 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.

Author
Damiano Fantini
Date of publication
2016-07-30 23:15:43
Maintainer
Damiano Fantini <damiano.fantini@gmail.com>
License
GPL-2
Version
1.3

View on CRAN

Man pages

basic_tcga_query
TCGA Core Query Engine
expand_cases
Explode TCGA Case Identifiers from a TCGA Study
fetch_all_tcgadata
Recursively Fetch All Data Included in a TCGA Study Subset
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...
get_case_lists
Retrieve All Case List Available for a Specific TCGA Study
get_clinical_data
Retrieve Clinical Information from a TCGA Study
get_ext_mutation
Retrieve Extended Information About DNA Mutations from TCGA
get_genetic_profiles
Retrieve Genetic Profiles for a TCGA Study of Interest
get_profile_data
Retrieve TCGA Data corresponding to a Specific Genetic...
get_protein_data
Retrieve Protein Expression Data from a TCGA Study
get_protein_info
Retrieve Information on Antibodies Used for Protein Levels...
make_groups
Split Numeric Vectors in Groups
TCGAretriever-package
Retrieve Genomic and Clinical Data from TCGA
trim_rnaseq_tcgadata
RNAseq Expression Data Trimmer

Files in this package

TCGAretriever
TCGAretriever/NAMESPACE
TCGAretriever/R
TCGAretriever/R/get_profile_data.R
TCGAretriever/R/get_cancer_studies.R
TCGAretriever/R/basic_tcga_query.R
TCGAretriever/R/get_protein_info.R
TCGAretriever/R/get_protein_data.R
TCGAretriever/R/get_case_lists.R
TCGAretriever/R/get_ext_mutation.R
TCGAretriever/R/expand_cases.R
TCGAretriever/R/TCGAretriever-internal.R
TCGAretriever/R/trim_rnaseq_tcgadata.R
TCGAretriever/R/get_genetic_profiles.R
TCGAretriever/R/get_cancer_types.R
TCGAretriever/R/fetch_all_tcgadata.R
TCGAretriever/R/get_clinical_data.R
TCGAretriever/R/make_groups.R
TCGAretriever/MD5
TCGAretriever/DESCRIPTION
TCGAretriever/man
TCGAretriever/man/get_case_lists.Rd
TCGAretriever/man/get_profile_data.Rd
TCGAretriever/man/get_protein_info.Rd
TCGAretriever/man/get_cancer_types.Rd
TCGAretriever/man/fetch_all_tcgadata.Rd
TCGAretriever/man/trim_rnaseq_tcgadata.Rd
TCGAretriever/man/make_groups.Rd
TCGAretriever/man/get_protein_data.Rd
TCGAretriever/man/expand_cases.Rd
TCGAretriever/man/get_cancer_studies.Rd
TCGAretriever/man/basic_tcga_query.Rd
TCGAretriever/man/get_clinical_data.Rd
TCGAretriever/man/TCGAretriever-package.Rd
TCGAretriever/man/get_genetic_profiles.Rd
TCGAretriever/man/get_ext_mutation.Rd