This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see diffHic.
Bioconductor version: 3.7
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 <alun at wehi.edu.au>
Maintainer: Aaron Lun <alun at wehi.edu.au>
Citation (from within R,
enter citation("diffHic")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("diffHic")
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 | ||
Text | NEWS |
biocViews | Alignment, Clustering, Coverage, HiC, MultipleComparison, Normalization, Preprocessing, Sequencing, Software |
Version | 1.12.1 |
In Bioconductor since | BioC 3.1 (R-3.2) (3.5 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 |
LinkingTo | Rhtslib(>= 1.12.1), zlibbioc, Rcpp |
Suggests | BSgenome.Ecoli.NCBI.20080805, Matrix |
SystemRequirements | C++11 |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | diffHic_1.12.1.tar.gz |
Windows Binary | diffHic_1.12.1.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | diffHic_1.12.1.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/diffHic |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/diffHic |
Package Short Url | http://bioconductor.org/packages/diffHic/ |
Package Downloads Report | Download Stats |
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