BCRANK: Predicting binding site consensus from ranked DNA sequences

Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BCRANK")
AuthorAdam Ameur <Adam.Ameur@genpat.uu.se>
Bioconductor views GeneRegulation MotifDiscovery
Date of publicationNone
MaintainerAdam Ameur <Adam.Ameur@genpat.uu.se>
LicenseGPL-2
Version1.38.0

View on Bioconductor

Functions

bcrank Man page
BCRANKmatch Man page
BCRANKmatch-class Man page
BCRANKout Man page
BCRANKresult Man page
BCRANKresult-class Man page
bcrankScore Man page
bcrankScore,BCRANKmatch-method Man page
BCRANKsearch Man page
BCRANKsearch-class Man page
consensus Man page
consensus,BCRANKmatch-method Man page
fname Man page
fname,BCRANKresult-method Man page
matchingSites Man page
matchVector Man page
matchVector,BCRANKmatch-method Man page
plot,BCRANKsearch,missing-method Man page
pwm Man page
pwm,BCRANKsearch-method Man page
searchPath Man page
searchPath,BCRANKsearch-method Man page
show,BCRANKmatch-method Man page
show,BCRANKresult-method Man page
show,BCRANKsearch-method Man page
toptable Man page
toptable,BCRANKresult-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/AllGenerics.R R/BCRANK.R R/methods-BCRANKmatch.R R/methods-BCRANKresult.R R/methods-BCRANKsearch.R
build
build/vignette.rds
data
data/BCRANKout.rda
inst
inst/Exfiles
inst/Exfiles/USF1_small.fa
inst/doc
inst/doc/BCRANK.R
inst/doc/BCRANK.Rnw
inst/doc/BCRANK.pdf
man
man/BCRANK-internal.Rd man/BCRANKmatch-class.Rd man/BCRANKout.Rd man/BCRANKresult-class.Rd man/BCRANKsearch-class.Rd man/bcrank.Rd man/matchingSites.Rd
src
src/init.c
src/match_consensus.c
src/match_consensus.h
vignettes
vignettes/BCRANK.Rnw
vignettes/BCRANK_intro_fig1.pdf
vignettes/BCRANK_intro_fig2.pdf

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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