diffHic
This is the development version of diffHic; for the stable release version, see diffHic.
Differential Analysis of Hi-C Data
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.45.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 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
Follow Installation instructions to use this package in your R session.
| Source Package | diffHic_1.45.0.tar.gz |
| Windows Binary (x86_64) | diffHic_1.45.0.zip |
| macOS Binary (big-sur-x86_64) | diffHic_1.45.0.tgz |
| macOS Binary (sonoma-arm64) | diffHic_1.45.0.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 |