diffHic
This is thereleased version of diffHic; for the devel version, seediffHic.
Differential Analysis of Hi-C Data
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("diffHic")For older versions of R, please refer to the appropriateBioconductor 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 | 1.42.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (10.5 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),Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | OHCA,hicream |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | diffHic_1.42.0.tar.gz |
| Windows Binary (x86_64) | diffHic_1.42.0.zip |
| macOS Binary (x86_64) | diffHic_1.42.0.tgz |
| macOS Binary (arm64) | diffHic_1.42.0.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 |