Store and query public TCGA data
Project description
pytcga
Python library for accessing and processing public TCGA data
Examples
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 mutations
luad_rnaseq = \
pytcga.load_rnaseq_data(disease_code='LUAD', with_clinical=True)
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Source Distribution
pytcga-0.0.4.tar.gz
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