Bioconductor version: Release (3.11)
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 [aut, cre], Kellen Cresswell [aut], Mikhail Dozmorov [aut]
Maintainer: John Stansfield <stansfieldjc at vcu.edu>
Citation (from within R,
enter citation("HiCcompare")
):
To install this package, start R (version "4.0") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("HiCcompare")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HiCcompare")
HTML | R Script | HiCcompare Usage Vignette |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | HiC, Normalization, Sequencing, Software |
Version | 1.10.0 |
In Bioconductor since | BioC 3.6 (R-3.4) (3 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 |
LinkingTo | |
Suggests | knitr, rmarkdown, testthat, multiHiCcompare |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | multiHiCcompare, SpectralTAD |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | HiCcompare_1.10.0.tar.gz |
Windows Binary | HiCcompare_1.10.0.zip |
macOS 10.13 (High Sierra) | HiCcompare_1.10.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/HiCcompare |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HiCcompare |
Package Short Url | https://bioconductor.org/packages/HiCcompare/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.11 | Source Archive |
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