DOI: 10.18129/B9.bioc.HiCcompare    

HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

Bioconductor version: Release (3.6)

HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust permutation method for detecting differences between Hi-C datasets.

Author: John Stansfield [aut, cre], Mikhail Dozmorov [aut]

Maintainer: John Stansfield <stansfieldjc at vcu.edu>

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biocViews HiC, Normalization, Sequencing, Software
Version 1.0.0
License MIT + file LICENSE
Depends R (>= 3.4.0), dplyr
Imports data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, QDNAseq, KernSmooth, methods, utils, graphics, pheatmap, gtools
Suggests knitr, rmarkdown, testthat
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