HiCcompare
HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
Bioconductor version: Release (3.19)
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: Mikhail Dozmorov [aut, cre] , Kellen Cresswell [aut], John Stansfield [aut]
Maintainer: Mikhail Dozmorov <mikhail.dozmorov at gmail.com>
citation("HiCcompare")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | HiC, Normalization, Sequencing, Software |
Version | 1.26.0 |
In Bioconductor since | BioC 3.6 (R-3.4) (7 years) |
License | MIT + file LICENSE |
Depends | R (>= 3.5.0), dplyr |
Imports | data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5 |
System Requirements | |
URL | https://github.com/dozmorovlab/HiCcompare |
Bug Reports | https://github.com/dozmorovlab/HiCcompare/issues |
See More
Suggests | knitr, rmarkdown, testthat, multiHiCcompare |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | multiHiCcompare, SpectralTAD, TADCompare |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | HiCcompare_1.26.0.tar.gz |
Windows Binary | HiCcompare_1.26.0.zip |
macOS Binary (x86_64) | HiCcompare_1.26.0.tgz |
macOS Binary (arm64) | HiCcompare_1.26.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/HiCcompare |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HiCcompare |
Bioc Package Browser | https://code.bioconductor.org/browse/HiCcompare/ |
Package Short Url | https://bioconductor.org/packages/HiCcompare/ |
Package Downloads Report | Download Stats |