diffHic (original) (raw)
This is the released version of diffHic; for the devel version, seediffHic.
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 , Hannah Coughlin <coughlin.h at wehi.edu.au>
Citation (from within R, enter 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 (64-bit only) |
| 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 |