motifRG: A package for discriminative motif discovery, designed for high throughput sequencing dataset
Version 1.20.0

Tools for discriminative motif discovery using regression methods

Browse man pages Browse package API and functions Browse package files

AuthorZizhen Yao
Bioconductor views MotifDiscovery Transcription
Date of publicationNone
MaintainerZizhen Yao <yzizhen@fhcrc.org>
LicenseArtistic-2.0
Version1.20.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("motifRG")

Man pages

ctcf.motifs: CTCF motifs predicted by motifRG
findMotif: De-novo discovery of distriminative motifs
findMotifFasta: Wrapper function for findMotif using fasta input
findMotifFgBg: Wrapper function for findMotif using two sequence datasets
getSequence: Fetch genomic sequences from GRanges Object
Motif: Motif objects
motifLatexTable: create of table of motifs
plotMotif: plot motif sequence matches
refinePWMMotif: create a PWM (Position Weight Model) model given a initial...
refinePWMMotifExtend: create an extended PWM (Position Weight Model) model given a...
summaryMotif: summarize a list of motifs
YY1.control: Background for YY1 ChIP-Seq peaks in HepG2
YY1.peak: YY1 ChIP-Seq peaks in HepG2

Functions

Motif-class Man page
YY1.control Man page
YY1.peak Man page
addGap Source code
addReversecomplement Source code
appendNucleotides Source code
bestPWMMatch Source code
bestPWMMatchCoor Source code
class:Motif Man page
combineReversecomplement Source code
consensus Source code
countNmer Source code
countSet Source code
countSetGeneral Source code
ctcf.motifs Man page
degeneratePattern Source code
discretize.glm Source code
entropy Source code
enumerateNmer Source code
expandPattern Source code
findMotif Man page Source code
findMotifFasta Man page Source code
findMotifFgBg Man page Source code
findPatternView Source code
getPWM Source code
getScore Source code
getScore.bootStrap Source code
getSequence Man page Source code
isContained Source code
isPalindrome Source code
logPWM Source code
maskPattern Source code
matchPWMCoor Source code
motifHtmlTable Man page Source code
motifLatexTable Man page Source code
motifScore Source code
my.pvec Source code
pasteSeq Source code
patternInfo Source code
plotMotif Man page Source code
plotPWM Source code
plotPair Source code
polyn Source code
reduceReversecomplement Source code
refinePWMMotif Man page Source code
refinePWMMotifExtend Man page Source code
relativeEntropy Source code
scanPWMMatch Source code
seqToMatrix Source code
split.pwm Source code
summaryMotif Man page Source code
trimPattern Source code

Files

DESCRIPTION
NAMESPACE
R
R/motif.rg.R
R/pwm.model.R
R/seq.util.R
build
build/vignette.rds
data
data/YY1.control.rda
data/YY1.peak.rda
data/ctcf.motifs.rda
inst
inst/Scripts
inst/Scripts/analysis.R
inst/css
inst/css/header.html
inst/doc
inst/doc/motifRG.R
inst/doc/motifRG.Rnw
inst/doc/motifRG.pdf
inst/extdata
inst/extdata/MD.control.fa
inst/extdata/MD.peak.fa
inst/extdata/ctcf.fa
man
man/Motif.Rd
man/YY1.control.Rd
man/YY1.peak.Rd
man/ctcf.motifs.Rd
man/findMotif.Rd
man/findMotifFasta.Rd
man/findMotifFgBg.Rd
man/getSequence.Rd
man/motifLatexTable.Rd
man/plotMotif.Rd
man/refinePWMMotif.Rd
man/refinePWMMotifExtend.Rd
man/summaryMotif.Rd
vignettes
vignettes/motifRG.Rnw
motifRG documentation built on May 20, 2017, 11 p.m.