diffHic
Differential Analysis of Hi-C Data
Bioconductor version: 3.23 · Package version: 1.44.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("diffHic")Details
| Maintainer | Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>, Gordon Smyth <smyth@wehi.edu.au>, Hannah Coughlin <coughlin.h@wehi.edu.au> |
| Author | Aaron Lun, Gordon Smyth |
| License | GPL-3 |
| System Requirements | C++, GNU make |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Clustering, Coverage, HiC, MultipleComparison, Normalization, Preprocessing, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/diffHic/ |
Citation
From within R, enter citation("diffHic"):
Aaron Lun, Gordon Smyth. diffHic: Differential Analysis of Hi-C Data. doi:10.18129/B9.bioc.diffHic, R package version 1.44.0, https://bioconductor.org/packages/diffHic.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | diffHic_1.44.0.tar.gz |
| Windows binary (x86_64) | diffHic_1.44.0.zip |
| macOS binary (arm64) | diffHic_1.44.0.tgz |
| macOS binary (x86_64) | diffHic_1.44.0.tgz |
Dependencies
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
LinkingTo: Rhtslib (>= 1.13.1), Rcpp
Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix, testthat
Reverse dependencies
Imports Me (1): hicream