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Last data update: 2014.03.03

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GADEM (Package: rGADEM) : Motif Analysis with rGADEM

It is an R implementation of GADEM, a powerful computational tools for de novo motif discovery.

● Data Source: BioConductor
● Keywords: GADEM, MOTIFS
● Alias: GADEM
● 0 images

align-class (Package: rGADEM) : Class "align"

This object contains the individual motifs identified but also the location (seqID and position) of the sites in the original sequence data. It also included the spaced dyad from which the motifs is derived, PWM score p-value cuttoff for the run.

● Data Source: BioConductor
● Keywords: classes
● Alias: align, align-class
● 0 images

gadem-class (Package: rGADEM) : Class "gadem"

This object contains all gadem output information.

● Data Source: BioConductor
● Keywords: classes
● Alias: [,gadem,ANY,ANY-method, [,gadem-method, [[,gadem,ANY,ANY-method, [[,gadem-method, consensus, consensus,gadem-method, dim,gadem-method, endPos, endPos,gadem-method, gadem, gadem-class, getPWM, getPWM,gadem-method, getPWM,motif-method, length,gadem-method, nMotifs,gadem-method, nOccurrences, nOccurrences,gadem-method, names,gadem-method, names<-,gadem-method, parameters,gadem-method, plot,gadem,ANY-method, plot,gadem-method, plot,motif,ANY-method, startPos, startPos,gadem-method, summary,list-method
● 0 images

motif-class (Package: rGADEM) : Class "motif"

This object contains contains PWM, motif consensus, motif length and all aligned sequences for a specific motif

● Data Source: BioConductor
● Keywords: classes
● Alias: motif, motif-class, nMotifs
● 0 images

parameters-class (Package: rGADEM) : Class "parameters"

This object contains contains parameters of GADEM analysis

● Data Source: BioConductor
● Keywords: classes
● Alias: parameters, parameters-class
● 0 images

readPWMfile (Package: rGADEM) : Read Transfac File

This function is use to read standard Transfac type file.

● Data Source: BioConductor
● Keywords: misc
● Alias: readPWMfile
● 0 images