Set of tools and pipelines to analyse GDSC data (cancerrxgene.org)
Project description
- Note:
tested for Python 2.7, 3.3, 3.4
- Contributions:
Please join https://github.com/CancerRxGene/gdsctools project
- Online documentation:
- Issues and bug reports:
Overview
Genomics of Drug Sensitivity in Cancer (GDSC) tools including pipelines related to http://www.cancerrxgene.org/
Installation
pip install gdsctools
For beginners, please visit the main documentation Installation section.
QuickStart
You will need 2 input matrices:
an IC50 matrix with COSMIC identifiers as rows and drugs as columns,
a genomic feature matrix with COSMIC identifiers as rows and features as columns.
Then, you can analyse the data with the standalone application:
gdsctools_anova --input-ic50 ic50.txt --input-features features.txt
or as a script:
from gdsctools import anova, ic50_test an = ANOVA(ic50_test, features_filename) # second arg is optional an.anova_all()
More examples are provided in the documentation on ReadThedoc. You can for example select a specific drug, or a set of drugs instead of the entire screening, or perform a sub selection on features.
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