MatrixRider

DOI: 10.18129/B9.bioc.MatrixRider    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MatrixRider.

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

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MatrixRider")

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.16.0
In Bioconductor since	BioC 3.1 (R-3.2) (4.5 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
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MatrixRider_1.16.0.tar.gz
Windows Binary	MatrixRider_1.16.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	MatrixRider_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MatrixRider
Source Repository (Developer Access)	git clone [email protected]:packages/MatrixRider
Package Short Url	https://bioconductor.org/packages/MatrixRider/
Package Downloads Report	Download Stats