Recent technological advances allow the measurement, in a single Hi-C experiment, of the frequencies of physical contacts among pairs of genomic loci at a genome-wide scale.
Iced implements a fast and memory efficient of the ICE normalization
strategy. It is included in the HiC-pro pipeline, that processes data from raw
fastq files to normalized contact maps. iced grew bigger than just
being a normalization packages, and contains a number of utilities functions
that may be useful if you are analyzing and processing Hi-C data.
.. toctree:: :maxdepth: 2
If you use iced as part of HiC-Pro, please cite:
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing *N. Servant, N. Varoquaux, B.R. Lajoie, E. Viara, C.J. Chen, J.-P. Vert, E. Heard, J. Dekker, E. Barillot, Genome Biology 2015
else, please cite:
iced: fast and memory efficient normalization of contact maps, N. Varoquaux, N. Servant, JOSS, 2019
If you have any questions or suggestions, please email nelle dot varoquaux at ensmp dot fr, or open a ticket on Github