HiCcompare

This package is for version 3.13 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: 3.13

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>

Citation (from within R, enter citation("HiCcompare")):

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("HiCcompare")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("HiCcompare")

HiCcompare Usage Vignette HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews HiC, Normalization, Sequencing, Software

Version 1.14.0

In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)

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, rhdf5

System Requirements

URL https://github.com/dozmorovlab/HiCcompare

Bug Reports https://github.com/dozmorovlab/HiCcompare/issues

Suggests knitr, rmarkdown, testthat, multiHiCcompare

Linking To

Enhances

Depends On Me

Imports Me multiHiCcompare, SpectralTAD, TADCompare

Suggests Me

Links To Me

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