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MatrixRider

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

Bioconductor version: Release (3.17)

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 (version "4.3") and enter:

if (!require("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")
Total affinity and occupancies PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneRegulation, Genetics, MotifAnnotation, Software
Version 1.32.0
In Bioconductor since BioC 3.1 (R-3.2) (8.5 years)
License GPL-3
Depends R (>= 3.1.2)
Imports methods, TFBSTools, IRanges, XVector, Biostrings
Linking To IRanges, XVector, Biostrings, S4Vectors
Suggests RUnit, BiocGenerics, BiocStyle, JASPAR2014
System Requirements
Enhances
URL
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Build Report  

Package Archives

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

Source Package MatrixRider_1.32.0.tar.gz
Windows Binary MatrixRider_1.32.0.zip
macOS Binary (x86_64) MatrixRider_1.32.0.tgz
macOS Binary (arm64) MatrixRider_1.32.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MatrixRider
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MatrixRider
Bioc Package Browser https://code.bioconductor.org/browse/MatrixRider/
Package Short Url https://bioconductor.org/packages/MatrixRider/
Package Downloads Report Download Stats