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cancer-hic-norm

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

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Normalization of cancer Hi-C data

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