DOI: 10.18129/B9.bioc.MatrixRider    

This package is for version 3.8 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: 3.8

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>

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biocViews GeneRegulation, Genetics, MotifAnnotation, Software
Version 1.14.0
In Bioconductor since BioC 3.1 (R-3.2) (4 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
Depends On Me
Imports Me
Suggests Me
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