README.txt

Topological data Analysis for array CGH (TAaCGH)


This is a repository with all the necessary scripts to run TAaCGH, a topological based method to analyze aCGH data whose output are regions of the genome where copy number is altered in patients with a predetermined cancer phenotype. We call this method Topological Analysis of array CGH.

For more information about the method please refer to DeWoskin et al 2010, Arsuaga et al 2015, Ardanza-Trevijano et al. 2016, Gonzalez et al 2018.

Details about how to use these scripts can be found in TAaCGH_Manual.docx

REFERENCES
+ Sergio Ardanza-Trevijano, Georgina Gonzalez, Tyler Borrman, Juan Luis Garcia, and Javier Arsuaga. Topological analysis of amplicon structure in comparative genomic hybridization (cgh) data: an application to erbb2/her2/neu amplified tumors. In International Workshop on Computational Topology in Image Context, pages 113–129. Springer, 2016
+ Javier Arsuaga, Tyler Borrman, Raymond Cavalcante, Georgina Gonzalez, and Catherine Park. Identification of copy number aberrations in breast cancer subtypes using persistence topology. Microarrays, 4(3):339–369, 2015.
+ Daniel DeWoskin, Joan Climent, I Cruz-White, Mariel Vazquez, Catherine Park, and Javier Arsuaga. Applications of computational homology to the analysis of treatment response in breast cancer patients. Topology and its Applications, 157(1):157–164, 2010
+ Gonzalez, Georgina, Arina Ushakova, Radmila Sazdanovic, and Javier Arsuaga. "Prediction in Cancer Genomics Using Topological Signatures and Machine Learning." In Topological Data Analysis, pp. 247-276. Springer, Cham, 2020.