gdsctools 0.9.5

Set of tools and pipelines to analyse GDSC data (cancerrxgene.org)

Note:

tested for Python 2.7, 3.3, 3.4

Contributions:

Please join https://github.com/CancerRxGene/gdsctools project

Online documentation:

On ReadTheDocs

Issues and bug reports:

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. 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.

Note

Version 1 (linear regression and ANOVA) was created based on https://github.com/francescojm/FI.GDSC.ANOVA repository.