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MotIV (version 1.28.0)

Motif Identification and Validation

Description

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.

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Version

Version

1.28.0

License

GPL-2

Maintainer

Eloi Mercier

Last Published

February 15th, 2017

Functions in MotIV (1.28.0)

filter-class

Class "filter"
jaspar2010

Jaspar 2010 Database
setFilter

Set Motif Filter
filter

Filter Motifs
FOXA1_rGADEM

Dataset for FOXA1
getGademPWM

Recover PWM
getPWM

Get PWMs from a motiv object
occurences

Motifs Occurences and Co-occurences
combineMotifs

Combine Motifs
filters-methods

Filters Methods
generateDBScores

Database Scores Functions
transcriptionFactor-class

Transcription Factor Class
readPWMfile

Read Transfac File
motifMatch

Motifs Matches Analysis
readGademPWMFile

Read Gadem File
viewAlignments

Print Motifs Alignments
motiv-class

Class "motiv"
motifDistances

Clustering PWMs Computation
plot-methods

Plot Motiv
exportAsTransfacFile

Write Transfac Files
makePWM

Constructing a pwm object
motiv-methods

Motiv methods
alignments-class

Class "alignments"
matches-class

Class "matches"
exportAsRangedData

Export MotIV Results
as.data.frame

Coerce to a Data Frame
viewMotifs-methods

Print Identified Motifs
trimPWMedge

Trim PWM edge
split-methods

Split Motiv Object
seqLogo2

Plot a sequence logo for a given position weight matrix