To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DNaseR")
In most cases, you don't need to download the package archive at all.
DNaseR
|
This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see DNaseR.
DNase I footprinting analysis of DNase-seq data
Bioconductor version: 3.0
Strand-specific digital genomic footprinting in 'double-hit' DNase-seq data. The cumulative Skellam distribution function (package 'skellam') is used to detect significant normalized count differences of opposed sign at each DNA strand. This is done in order to determine the protein-binding footprint flanks. Preprocessing of the mapped reads is recommended before running DNaseR (e.g., quality checking and removal of sequence-specific biases).
Author: Pedro Madrigal <pm12 at sanger.ac.uk>
Maintainer: Pedro Madrigal <pm12 at sanger.ac.uk>
Citation (from within R,
enter citation("DNaseR")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DNaseR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DNaseR")
| R Script | DNaseR Vignette | |
| Reference Manual | ||
| Text | LICENSE |
Details
| biocViews | Genetics, Software, Transcription |
| Version | 1.4.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (2.5 years) |
| License | GPL-2 + file LICENSE |
| Depends | R (>= 2.10.0), BiocGenerics, S4Vectors, IRanges |
| Imports | GenomeInfoDb, GenomicRanges, Rsamtools |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics |
| 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 | DNaseR_1.4.0.tar.gz |
| Windows Binary | DNaseR_1.4.0.zip |
| Mac OS X 10.6 (Snow Leopard) | DNaseR_1.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | DNaseR_1.4.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/DNaseR/tree/release-3.0 |
| Package Short Url | http://bioconductor.org/packages/DNaseR/ |
| Package Downloads Report | Download Stats |
Documentation »
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