multiHiCcompare
This is the development version of multiHiCcompare; for the stable release version, see multiHiCcompare.
Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Bioconductor version: Development (3.24)
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: Mikhail Dozmorov [aut, cre]
, John Stansfield [aut]
Maintainer: Mikhail Dozmorov <mikhail.dozmorov at gmail.com>
citation("multiHiCcompare")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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")| juiceboxVisualization | HTML | R Script |
| multiHiCcompare | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | HiC, Normalization, Sequencing, Software |
| Version | 1.31.1 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0.0) |
| Imports | data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, GenomeInfoDb, metap |
| System Requirements | |
| URL | https://github.com/dozmorovlab/multiHiCcompare |
| Bug Reports | https://github.com/dozmorovlab/multiHiCcompare/issues |
See More
| Suggests | knitr, rmarkdown, testthat, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | HiCDOC, OHCA |
| 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_1.31.1.tar.gz |
| Windows Binary (x86_64) | multiHiCcompare_1.31.1.zip |
| macOS Binary (big-sur-x86_64) | multiHiCcompare_1.31.1.tgz |
| macOS Binary (sonoma-arm64) | multiHiCcompare_1.31.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/multiHiCcompare |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/multiHiCcompare |
| Bioc Package Browser | https://code.bioconductor.org/browse/multiHiCcompare/ |
| Package Short Url | https://bioconductor.org/packages/multiHiCcompare/ |
| Package Downloads Report | Download Stats |