DEPRECATED

The TCGA API that this relied no longer exists and this project has been deprecated in favor of PyGDC

pytcga

Python library for accessing and processing public TCGA data

Examples

Getting a list of all TCGA studies

import pytcga

# Get a list of study names and their abbreviations
studies = pytcga.load_studies()

Loading Clinical Data

import pytcga

# Downloading and loading LUAD patient data
clinical = pytcga.load_clinical_data('luad')

Loading Mutation Data

import pytcga

# Downloading and loading LUAD mutations
luad_mutations = \
    pytcga.load_mutation_data(disease_code='LUAD', with_clinical=False)


# Also appends clinical data with `with_clinical` flag
luad_mutations = \
    pytcga.load_mutation_data(disease_code='LUAD', with_clinical=True)

# Filter variants with the `variant_type` argument
# variant_type = {'all', 'indel', SNP', 'INS', 'DEL'}
luad_indel_mutations = \
    pytcga.load_mutation_data(disease_code='LUAD', with_clinical=True, variant_type='indel')

Loading RNASeq Data

import pytcga

# Downloading and loading LUAD gene quantification
luad_rnaseq = \
    pytcga.load_rnaseq_data(disease_code='LUAD', with_clinical=True)