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

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
Date of publication
None
Maintainer
Elena Grassi <grassi.e@gmail.com>
License
GPL-3
Version
1.6.0

View on Bioconductor

Man pages

getSeqOccupancy-method
Computes the total affinity or the occupancy at a given...
MatrixRider-package
Calculate total affinity and occupancies for binding site...

Files in this package

MatrixRider/DESCRIPTION
MatrixRider/NAMESPACE
MatrixRider/R
MatrixRider/R/AllGenerics.R
MatrixRider/R/matrix_rider_methods.R
MatrixRider/build
MatrixRider/build/vignette.rds
MatrixRider/inst
MatrixRider/inst/NEWS
MatrixRider/inst/doc
MatrixRider/inst/doc/MatrixRider.R
MatrixRider/inst/doc/MatrixRider.Rnw
MatrixRider/inst/doc/MatrixRider.pdf
MatrixRider/inst/examples
MatrixRider/inst/examples/MatrixRiderWrapper.R
MatrixRider/inst/unitTests
MatrixRider/inst/unitTests/test_getSeqOccupancy.R
MatrixRider/man
MatrixRider/man/MatrixRider-package.Rd
MatrixRider/man/getSeqOccupancy-method.Rd
MatrixRider/src
MatrixRider/src/Biostring_stubs.c
MatrixRider/src/CuTest.c
MatrixRider/src/CuTest.h
MatrixRider/src/R_init_MatrixRider.c
MatrixRider/src/RunCuTest.c
MatrixRider/src/XVector_stubs.c
MatrixRider/src/matrix_rider.c
MatrixRider/src/total_affinity.h
MatrixRider/tests
MatrixRider/tests/runTests.R
MatrixRider/vignettes
MatrixRider/vignettes/MatrixRider.Rnw
MatrixRider/vignettes/biblio.bib