| 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 |
Genomics of Drug Sensitivity in Cancer (GDSC) tools including pipelines related to http://www.cancerrxgene.org/
pip install gdsctools
For beginners, please visit the main documentation Installation section.
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.
Note
Version 1 (linear regression and ANOVA) was created based on https://github.com/francescojm/FI.GDSC.ANOVA repository.