Tools related to the Genomics of Drug Sensitivity in Cancer (GDSC) projects (http://www.cancerrxgene.org/ )
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README.rst

GDSCTools

https://secure.travis-ci.org/CancerRxGene/gdsctools.png https://coveralls.io/repos/CancerRxGene/gdsctools/badge.svg?branch=master&service=github Documentation Status

BSD License

Citation:Cokelaer et al. GDSCTools for mining pharmacogenomic interactions in cancer. Bioinformatics, 2017, https://doi.org/10.1093/bioinformatics/btx744
Note:Developed and tested for Python 2.7, 3.5, 3.6
Note:The GDSCTools libary works for Python 2.7 and 3.X but the standalone pipeline to be ran on cluster works on Python 3.X only (requires Snakemake).
Contributions:Please join https://github.com/CancerRxGene/gdsctools project
Documentation:On ReadTheDocs
GitHub:On github

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:

  1. an IC50 matrix with COSMIC identifiers as rows and drugs as columns,
  2. 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.

Note that first versions (ANOVA analysis) were based on https://github.com/francescojm/FI.GDSC.ANOVA repository. New tools have been added (regression based on Ridge, Lasso, OmniBEM tool, ...).