Skip to main content

Store and query public TCGA data

Project description


Python library for accessing and processing public TCGA data


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)

Project details

Release history Release notifications

This version
History Node


History Node


History Node


History Node


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
pytcga-0.0.4.tar.gz (6.2 kB) Copy SHA256 hash SHA256 Source None Jan 17, 2016

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging CloudAMQP CloudAMQP RabbitMQ AWS AWS Cloud computing Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page