multiHiCcompare
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see multiHiCcompare.
Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Bioconductor version: 3.9
multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner.
Author: John Stansfield [aut, cre], Mikhail Dozmorov [aut]
Maintainer: John Stansfield <stansfieldjc at vcu.edu>
citation("multiHiCcompare")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("multiHiCcompare")
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("multiHiCcompare")| multiHiCcompare Vignette | HTML | R Script |
| Visualizing results in Juicebox | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | HiC, Normalization, Sequencing, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.0) |
| Imports | data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, metap, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, BLMA, GenomeInfoDb |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, testthat, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | HiCcompare |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | multiHiCcompare_1.2.0.tar.gz |
| Windows Binary | multiHiCcompare_1.2.0.zip |
| Mac OS X 10.11 (El Capitan) | multiHiCcompare_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/multiHiCcompare |
| Source Repository (Developer Access) | git clone [email protected]:packages/multiHiCcompare |
| Bioc Package Browser | https://code.bioconductor.org/browse/multiHiCcompare/ |
| Package Short Url | https://bioconductor.org/packages/multiHiCcompare/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |