HiCcompare
This is the released version of HiCcompare; for the devel version, see HiCcompare.
HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
Bioconductor version: Release (3.23)
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")):
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")
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 | 1.34.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 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, scHiCcompare, 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_1.34.0.tar.gz |
| Windows Binary (x86_64) | HiCcompare_1.34.0.zip |
| macOS Binary (big-sur-x86_64) | HiCcompare_1.34.0.tgz |
| macOS Binary (sonoma-arm64) | HiCcompare_1.34.0.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 |