MatrixRider

This is the released version of MatrixRider; for the devel version, see MatrixRider.

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

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DOI: 10.18129/B9.bioc.MatrixRider

Bioconductor version: Release (3.22)

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneRegulation, Genetics, MotifAnnotation, Software

Version 1.42.0

In Bioconductor since BioC 3.1 (R-3.2) (10.5 years)

License GPL-3

Depends R (>= 3.1.2)

Imports methods, TFBSTools, IRanges, XVector, Biostrings

System Requirements

URL

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_1.42.0.tar.gz

Windows Binary (x86_64) MatrixRider_1.42.0.zip

macOS Binary (x86_64) MatrixRider_1.42.0.tgz

macOS Binary (arm64) MatrixRider_1.42.0.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/

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