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.

AuthorEloi Mercier, Raphael Gottardo
Date of publicationNone
MaintainerEloi Mercier <emercier@bcgsc.ca>, Raphael Gottardo <rgottard@fhcrc.org>
LicenseGPL-2
Version1.30.0

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

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

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