To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MatrixRider")

In most cases, you don't need to download the package archive at all.

MatrixRider

 

Obtain total affinity and occupancies for binding site matrices on a given sequence

Bioconductor version: Release (3.5)

Calculates a single number for a whole sequence that reflects the propensity of a DNA binding protein to interact with it. The DNA binding protein has to be described with a PFM matrix, for example gotten from Jaspar.

Author: Elena Grassi

Maintainer: Elena Grassi <grassi.e at gmail.com>

Citation (from within R, enter citation("MatrixRider")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MatrixRider")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MatrixRider")

 

PDF R Script Total affinity and occupancies
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneRegulation, Genetics, MotifAnnotation, Software
Version 1.8.0
In Bioconductor since BioC 3.1 (R-3.2) (2.5 years)
License GPL-3
Depends R (>= 3.1.2)
Imports methods, TFBSTools, IRanges, XVector, Biostrings
LinkingTo IRanges, XVector, Biostrings, S4Vectors
Suggests RUnit, BiocGenerics, BiocStyle, JASPAR2014
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 MatrixRider_1.8.0.tar.gz
Windows Binary MatrixRider_1.8.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) MatrixRider_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MatrixRider
Package Short Url http://bioconductor.org/packages/MatrixRider/
Package Downloads Report Download Stats

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