diffHic
Differential Analysis of Hi-C Data
Bioconductor version: 3.24 · Package version: 1.45.0
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 |
| Downloads rank | 767 |
| Source branch | devel |
| biocViews | Alignment, Clustering, Coverage, HiC, MultipleComparison, Normalization, Preprocessing, Sequencing, Software |
Documentation
Download
Follow the 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 (arm64) | diffHic_1.45.0.tgz |
| macOS binary (x86_64) | diffHic_1.45.0.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