MotIV: Motif Identification and Validation

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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.

Author
Eloi Mercier, Raphael Gottardo
Date of publication
None
Maintainer
Eloi Mercier <emercier@bcgsc.ca>, Raphael Gottardo <rgottard@fhcrc.org>
License
GPL-2
Version
1.30.0

View on Bioconductor

Man pages

aligns-class
Class "alignments"
as.data.frame
Coerce to a Data Frame
combineMotifs
Combine Motifs
exportAsRangedData
Export MotIV Results
exportAsTransfacFile
Write Transfac Files
filter
Filter Motifs
filter-class
Class "filter"
filter-methods
Filters Methods
FOXA_rGADEM
Dataset for FOXA1
generateDBScores
Database Scores Functions
getGademPWM
Recover PWM
jaspar
Jaspar 2010 Database
makePWM
Constructing a pwm object
matches-class
Class "matches"
motifDistance
Clustering PWMs Computation
motifMatch
Motifs Matches Analysis
motifOccurences
Motifs Occurences and Co-occurences
motiv-class
Class "motiv"
motiv-methods
Motiv methods
plot
Plot Motiv
readGademPWMFile
Read Gadem File
readPWMfile
Read Transfac File
seqLogo2
Plot a sequence logo for a given position weight matrix
setFilter
Set Motif Filter
split
Split Motiv Object
tf-class
Transcription Factor Class
trimPWMedge
Trim PWM edge
viewAlignment
Print Motifs Alignments
viewMotifs
Print Identified Motifs

Files in this package

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