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motifRG (version 1.16.0)

A package for discriminative motif discovery, designed for high throughput sequencing dataset

Description

Tools for discriminative motif discovery using regression methods

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Version

Version

1.16.0

License

Artistic-2.0

Maintainer

Zizhen Yao

Last Published

February 15th, 2017

Functions in motifRG (1.16.0)

getSequence

Fetch genomic sequences from GRanges Object
findMotifFgBg

Wrapper function for findMotif using two sequence datasets
findMotif

De-novo discovery of distriminative motifs
summaryMotif

summarize a list of motifs
refinePWMMotif

create a PWM (Position Weight Model) model given a initial set of motif matches and input sequences
YY1.control

Background for YY1 ChIP-Seq peaks in HepG2
YY1.peak

YY1 ChIP-Seq peaks in HepG2
Motif-class

Motif objects
ctcf.motifs

CTCF motifs predicted by motifRG
plotMotif

plot motif sequence matches
motifLatexTable

create of table of motifs
refinePWMMotifExtend

create an extended PWM (Position Weight Model) model given a initial set of motif matches and input sequences
findMotifFasta

Wrapper function for findMotif using fasta input