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

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


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


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

Total affinity and occupancies PDF R Script
Reference Manual PDF


biocViews GeneRegulation, Genetics, MotifAnnotation, Software
Version 1.36.0
In Bioconductor since BioC 3.1 (R-3.2) (9.5 years)
License GPL-3
Depends R (>= 3.1.2)
Imports methods, TFBSTools, IRanges, XVector, Biostrings
System Requirements
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Suggests RUnit, BiocGenerics, BiocStyle, JASPAR2014
Linking To IRanges, XVector, Biostrings, S4Vectors
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Follow Installation instructions to use this package in your R session.

Source Package MatrixRider_1.36.0.tar.gz
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macOS Binary (x86_64) MatrixRider_1.36.0.tgz
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