diffHic
Differential Analysis of Hi-C Data
Bioconductor version: Release (3.20)
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, Gordon Smyth
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>, Gordon Smyth <smyth at wehi.edu.au>, Hannah Coughlin <coughlin.h at wehi.edu.au>
citation("diffHic")
):
Installation
To install this package, start R (version "4.4") 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 | 1.38.0 |
In Bioconductor since | BioC 3.1 (R-3.2) (9.5 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++, GNU make |
URL |
See More
Suggests | BSgenome.Ecoli.NCBI.20080805, Matrix, testthat |
Linking To | Rhtslib(>= 1.13.1), zlibbioc, Rcpp |
Enhances | |
Depends On Me | |
Imports Me | OHCA |
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_1.38.0.tar.gz |
Windows Binary (x86_64) | diffHic_1.38.0.zip |
macOS Binary (x86_64) | diffHic_1.38.0.tgz |
macOS Binary (arm64) | diffHic_1.38.0.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 |