GDSCTools

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|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 <http://gdsctools.readthedocs.io/en/master> :GitHub: On github <https://github.com/CancerRxGene/gdsctools/issues>

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 <http://gdsctools.readthedocs.io/en/master/installation.html>_ 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 <http://gdsctools.readthedocs.io/en/master/index.html>_.

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, ...).

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