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MatrixRider

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


Bioconductor version: Release (3.18)

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 1.34.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License GPL-3
Depends R (>= 3.1.2)
Imports methods, TFBSTools, IRanges, XVector, Biostrings
System Requirements
URL
See More
Suggests RUnit, BiocGenerics, BiocStyle, JASPAR2014
Linking To IRanges, XVector, Biostrings, S4Vectors
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package MatrixRider_1.34.0.tar.gz
Windows Binary MatrixRider_1.34.0.zip
macOS Binary (x86_64) MatrixRider_1.34.0.tgz
macOS Binary (arm64)
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/
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