Normalization of cancer Hi-C data
The project contains the scripts used in the manuscript : "Effective normalization for copy number variation in Hi-C data. Servant N, Varoquaux N, Heard E, Vert JP, Barillot E."
All results and data used in the publication are available at http://members.cbio.mines-paristech.fr/~nvaroquaux/normalization/
The sources are organized as follow :
- simulation_model
Contains the script to simulation cancer Hi-C data from diploid real Hi-C data
- cnv_from_hic
Contains the script to infer the CNV profile from any Hi-C dataset
- CNV_norm
Scripts to apply the LOIC and CAIC normalization.
Note that both methods are now included in the iced python package (>0.5.0).
In case of question, please contact ; nicolas.servant@curie.fr, nelle.varoquaux@gmail.com