diffHic
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see diffHic.
Differential Analyis of Hi-C Data
Bioconductor version: 3.9
Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.
Author: Aaron Lun [aut, cre], Gordon Smyth [aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("diffHic")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("diffHic")
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("diffHic")| diffHic Vignette | |
| diffHicUsersGuide.pdf | |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | Alignment, Clustering, Coverage, HiC, MultipleComparison, Normalization, Preprocessing, Sequencing, Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
| License | GPL-3 |
| Depends | R (>= 3.5), GenomicRanges, InteractionSet, SummarizedExperiment |
| Imports | Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma, csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb, BiocGenerics, grDevices, graphics, stats, utils, Rcpp, rtracklayer |
| System Requirements | C++11 |
| URL |
See More
| Suggests | BSgenome.Ecoli.NCBI.20080805, Matrix, testthat |
| Linking To | Rhtslib(>= 1.13.1), zlibbioc, Rcpp |
| 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 | diffHic_1.16.0.tar.gz |
| Windows Binary | diffHic_1.16.0.zip |
| Mac OS X 10.11 (El Capitan) | diffHic_1.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/diffHic |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/diffHic |
| Bioc Package Browser | https://code.bioconductor.org/browse/diffHic/ |
| Package Short Url | https://bioconductor.org/packages/diffHic/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |