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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MatrixRider")
AuthorElena Grassi
Bioconductor views GeneRegulation Genetics MotifAnnotation
Date of publicationNone
MaintainerElena Grassi <grassi.e@gmail.com>
LicenseGPL-3
Version1.8.0

View on Bioconductor

Functions

getSeqOccupancy Man page
getSeqOccupancy,DNAString,PFMatrixList,numeric-method Man page
getSeqOccupancy,DNAString,PFMatrix,numeric-method Man page
getSeqOccupancy-methods Man page
MatrixRider Man page
MatrixRider-package Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllGenerics.R R/matrix_rider_methods.R
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/MatrixRider.R
inst/doc/MatrixRider.Rnw
inst/doc/MatrixRider.pdf
inst/examples
inst/examples/MatrixRiderWrapper.R
inst/unitTests
inst/unitTests/test_getSeqOccupancy.R
man
man/MatrixRider-package.Rd man/getSeqOccupancy-method.Rd
src
src/Biostring_stubs.c
src/CuTest.c
src/CuTest.h
src/R_init_MatrixRider.c
src/RunCuTest.c
src/XVector_stubs.c
src/matrix_rider.c
src/total_affinity.h
tests
tests/runTests.R
vignettes
vignettes/MatrixRider.Rnw
vignettes/biblio.bib
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Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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