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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("diffHic")
In most cases, you don't need to download the package archive at all.
diffHic
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Differential Analyis of Hi-C Data
Bioconductor version: Release (3.4)
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")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("diffHic")
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 | ||
| Text | NEWS |
Details
| biocViews | Alignment, Clustering, Coverage, HiC, MultipleComparison, Normalization, Preprocessing, Sequencing, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (2 years) |
| License | GPL-3 |
| Depends | R (>= 3.3.0), GenomicRanges, InteractionSet, SummarizedExperiment |
| Imports | Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma, csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb, BiocGenerics, grDevices, graphics, stats, utils |
| LinkingTo | Rhtslib, zlibbioc |
| Suggests | BSgenome.Ecoli.NCBI.20080805, Matrix |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | diffHic_1.6.0.tar.gz |
| Windows Binary | diffHic_1.6.0.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | diffHic_1.6.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/diffHic/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/diffHic/ |
| Package Downloads Report | Download Stats |
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