HiCcompare
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see HiCcompare.
HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
Bioconductor version: 3.7
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 permutation method for detecting differences between Hi-C datasets.
Author: John Stansfield [aut, cre], Mikhail Dozmorov [aut]
Maintainer: John Stansfield <stansfieldjc at vcu.edu>
citation("HiCcompare")):
Installation
To install this package, start R (version "3.5") 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 | 1.2.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| 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_1.2.0.tar.gz |
| Windows Binary | HiCcompare_1.2.0.zip |
| Mac OS X 10.11 (El Capitan) | HiCcompare_1.2.0.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 3.7 | Source Archive |