MotIV: Motif Identification and Validation

This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MotIV")
AuthorEloi Mercier, Raphael Gottardo
Bioconductor views ChIPSeq ChIPchip GenomicSequence Microarray MotifAnnotation
Date of publicationNone
MaintainerEloi Mercier <emercier@bcgsc.ca>, Raphael Gottardo <rgottard@fhcrc.org>
LicenseGPL-2
Version1.32.0

View on Bioconductor

Functions

alignments-class Man page
as.data.frame Man page
as.data.frame-methods Man page
as.data.frame,motiv-method Man page
combineMotifs Man page
combineMotifs-method Man page
combineMotifs,motiv,filters-method Man page
combineMotifs,motiv,list-method Man page
cooccurences Man page
exportAsRangedData Man page
exportAsTransfacFile Man page
exportAsTransfacFile,list-method Man page
exportAsTransfacFile-methods Man page
exportAsTransfacFile,motiv-method Man page
filter Man page
filter-class Man page
filter-methods Man page
filter,motiv,filters-method Man page
filter,motiv,list-method Man page
|,filters,filters-method Man page
&,filters,filters-method Man page
FOXA Man page
FOXA1_rGADEM Man page
gadem Man page
generateDBScores Man page
getGademPWM Man page
jaspar Man page
jaspar.scores Man page
length,motiv-method Man page
makePWM Man page
matches-class Man page
motifCutree Man page
motifDistances Man page
motifHclust Man page
motifMatch Man page
motiv Man page
[,motiv,ANY,ANY-method Man page
motiv-class Man page
[,motiv-method Man page
names,filter-method Man page
names,filters-method Man page
names<-,motiv-method Man page
names,motiv-method Man page
occurences Man page
plot Man page
plot-methods Man page
plot,motiv,ANY-method Man page
plot,motiv,gadem-method Man page
plot,motiv,gadem-method Man page
plot,motiv-method Man page
readDBScores Man page
readGademPWMFile Man page
readPWMfile Man page
seqLogo2 Man page
setFilter Man page
show,filter-method Man page
show,motiv-method Man page
similarity Man page
similarity,list-method Man page
similarity,motiv-method Man page
split-methods Man page
split,motiv,filters-method Man page
split,motiv,list-method Man page
summary,filter-method Man page
summary,filters-method Man page
summary,list-method Man page
summary,motiv-method Man page
transcriptionFactor-class Man page
trimPWMedge Man page
viewAlignments Man page
viewMotifs Man page
viewMotifs-methods Man page
viewMotifs,motiv-method Man page
writeDBScores Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/AllMethods.R R/DBScores.R R/calculatePosition.R R/exportAsRangedData.R R/exportAsTransfacFile.R R/filterMotiv.R R/getGademPWM.R R/motifDistances.R R/motifMatch.R R/motifOccurences.R R/plotDistance.R R/plotDistribution.R R/plotMotiv.R R/readGademPWMFile.R R/readPWMfile.R R/seqLogo2.R R/trimPWMedge.R R/viewAlignment.R R/zzz.R
build
build/vignette.rds
configure
configure.ac
data
data/FOXA1_rGADEM.rda
data/jaspar2010.rda
data/jaspar2010_scores.rda
inst
inst/doc
inst/doc/MotIV.R
inst/doc/MotIV.Rnw
inst/doc/MotIV.pdf
inst/extdata
inst/extdata/example_motifs.txt
inst/extdata/jaspar2010.txt
inst/extdata/jaspar2010_PCC_SWU.scores
inst/extdata/observedPWMs.txt
man
man/FOXA_rGADEM.Rd man/aligns-class.Rd man/as.data.frame.Rd man/combineMotifs.Rd man/exportAsRangedData.Rd man/exportAsTransfacFile.Rd man/filter-class.Rd man/filter-methods.Rd man/filter.Rd man/generateDBScores.Rd man/getGademPWM.Rd
man/getPWM.rd
man/jaspar.Rd man/makePWM.Rd man/matches-class.Rd man/motifDistance.Rd man/motifMatch.Rd man/motifOccurences.Rd man/motiv-class.Rd man/motiv-methods.Rd man/plot.Rd man/readGademPWMFile.Rd man/readPWMfile.Rd man/seqLogo2.Rd man/setFilter.Rd man/split.Rd man/tf-class.Rd man/trimPWMedge.Rd man/viewAlignment.Rd man/viewMotifs.Rd
src
src/Alignment.cpp
src/Alignment.h
src/ColumnComp.cpp
src/ColumnComp.h
src/DeclareAll.cpp
src/Makevars
src/Makevars.in
src/Makevars.win
src/Motif.cpp
src/Motif.h
src/MotifDistances.cpp
src/MotifMatch.cpp
src/PSSM.h
src/PlatformSupport.cpp
src/PlatformSupport.h
src/RandPSSMGen.cpp
src/RandPSSMGen.h
src/generateScoresDB.cpp
src/globals.h
vignettes
vignettes/MotIV.Rnw

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

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