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

Tools for discriminative motif discovery using regression methods

Author
Zizhen Yao
Date of publication
None
Maintainer
Zizhen Yao <yzizhen@fhcrc.org>
License
Artistic-2.0
Version
1.18.0

View on Bioconductor

Man pages

ctcf.motifs
CTCF motifs predicted by motifRG
findMotif
De-novo discovery of distriminative motifs
findMotifFasta
Wrapper function for findMotif using fasta input
findMotifFgBg
Wrapper function for findMotif using two sequence datasets
getSequence
Fetch genomic sequences from GRanges Object
Motif
Motif objects
motifLatexTable
create of table of motifs
plotMotif
plot motif sequence matches
refinePWMMotif
create a PWM (Position Weight Model) model given a initial...
refinePWMMotifExtend
create an extended PWM (Position Weight Model) model given a...
summaryMotif
summarize a list of motifs
YY1.control
Background for YY1 ChIP-Seq peaks in HepG2
YY1.peak
YY1 ChIP-Seq peaks in HepG2

Files in this package

motifRG/DESCRIPTION
motifRG/NAMESPACE
motifRG/R
motifRG/R/motif.rg.R
motifRG/R/pwm.model.R
motifRG/R/seq.util.R
motifRG/build
motifRG/build/vignette.rds
motifRG/data
motifRG/data/YY1.control.rda
motifRG/data/YY1.peak.rda
motifRG/data/ctcf.motifs.rda
motifRG/inst
motifRG/inst/Scripts
motifRG/inst/Scripts/analysis.R
motifRG/inst/css
motifRG/inst/css/header.html
motifRG/inst/doc
motifRG/inst/doc/motifRG.R
motifRG/inst/doc/motifRG.Rnw
motifRG/inst/doc/motifRG.pdf
motifRG/inst/extdata
motifRG/inst/extdata/MD.control.fa
motifRG/inst/extdata/MD.peak.fa
motifRG/inst/extdata/ctcf.fa
motifRG/man
motifRG/man/Motif.Rd
motifRG/man/YY1.control.Rd
motifRG/man/YY1.peak.Rd
motifRG/man/ctcf.motifs.Rd
motifRG/man/findMotif.Rd
motifRG/man/findMotifFasta.Rd
motifRG/man/findMotifFgBg.Rd
motifRG/man/getSequence.Rd
motifRG/man/motifLatexTable.Rd
motifRG/man/plotMotif.Rd
motifRG/man/refinePWMMotif.Rd
motifRG/man/refinePWMMotifExtend.Rd
motifRG/man/summaryMotif.Rd
motifRG/vignettes
motifRG/vignettes/motifRG.Rnw