DOI: 10.18129/B9.bioc.HiCcompare  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see HiCcompare.

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

Bioconductor version: 3.16

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 method for detecting differences between Hi-C datasets.

Author: John Stansfield <stansfieldjc at vcu.edu>, Kellen Cresswell <cresswellkg at vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov at vcuhealth.org>

Maintainer: John Stansfield <stansfieldjc at vcu.edu>, Mikhail Dozmorov <mikhail.dozmorov at vcuhealth.org>

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biocViews HiC, Normalization, Sequencing, Software
Version 1.20.0
In Bioconductor since BioC 3.6 (R-3.4) (5.5 years)
License MIT + file LICENSE
Depends R (>= 3.5.0), dplyr
Imports data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, QDNAseq, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5
Suggests knitr, rmarkdown, testthat, multiHiCcompare
URL https://github.com/dozmorovlab/HiCcompare
BugReports https://github.com/dozmorovlab/HiCcompare/issues
Depends On Me
Imports Me multiHiCcompare, SpectralTAD, TADCompare
Suggests Me
Links To Me
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Source Package HiCcompare_1.20.0.tar.gz
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