motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.

AuthorJianhong Ou, Michael Brodsky, Scot Wolfe and Lihua Julie Zhu
Date of publicationNone
MaintainerJianhong Ou <jianhong.ou@umassmed.edu>
LicenseGPL (>= 2)
Version1.18.0

View on Bioconductor

Functions

addBlank Man page
addBlank,pcm,numeric,logical-method Man page
addBlank,pfm,numeric,logical-method Man page
colorset Man page
DNAmotifAlignment Man page
frequence Man page
frequence,motifSig-method Man page
getIC Man page
getIC,matrix,matrix-method Man page
getIC,matrix,numeric-method Man page
getIC,pcm,ANY-method Man page
getIC,pfm,ANY-method Man page
getRankedUniqueMotifs Man page
highlightCol Man page
matrixReverseComplement Man page
matrixReverseComplement,pcm-method Man page
matrixReverseComplement,pfm-method Man page
mergeMotifs Man page
motifCircos Man page
motifCloud Man page
motifPiles Man page
motifSig Man page
motifSig-class Man page
$<-,motifSig-method Man page
$,motifSig-method Man page
motifSignature Man page
motifStack Man page
motifStack-package Man page
nodelist Man page
nodelist,motifSig-method Man page
ouNode Man page
ouNode-class Man page
$<-,ouNode-method Man page
$,ouNode-method Man page
pcm Man page
pcm2pfm Man page
pcm2pfm,data.frame,ANY-method Man page
pcm2pfm,data.frame,numeric-method Man page
pcm2pfm,matrix,ANY-method Man page
pcm2pfm,matrix,numeric-method Man page
pcm2pfm,pcm,ANY-method Man page
pcm-class Man page
$<-,pcm-method Man page
$,pcm-method Man page
pfm Man page
pfm2pwm Man page
pfm-class Man page
$<-,pfm-method Man page
$,pfm-method Man page
plotMotifLogo Man page
plotMotifLogoA Man page
plotMotifLogoStack Man page
plotMotifLogoStackWithTree Man page
plotMotifOverMotif Man page
plotMotifStackWithPhylog Man page
plotMotifStackWithRadialPhylog Man page
plot,pcm,ANY-method Man page
plot,pfm,ANY-method Man page
plotXaxis Man page
plotYaxis Man page
readPCM Man page
reorderUPGMAtree Man page
sigColor Man page
sigColor,motifSig-method Man page
signatures Man page
signatures,motifSig-method Man page
trimMotif Man page
trimMotif,pcm,numeric-method Man page
trimMotif,pfm,numeric-method Man page

Files

motifStack/DESCRIPTION
motifStack/NAMESPACE
motifStack/NEWS
motifStack/R
motifStack/R/getRankedUniqueMotifs.R motifStack/R/mergeMotifs.R motifStack/R/motifCircos.R motifStack/R/motifPiles.R motifStack/R/motifStack.R motifStack/R/pcm.R motifStack/R/pfm.R motifStack/R/plotMotifOverMotif.R motifStack/R/privateUtilities.R motifStack/R/publicUtilities.R motifStack/R/reorderUPGMAtree.R motifStack/R/signature.R
motifStack/build
motifStack/build/vignette.rds
motifStack/inst
motifStack/inst/doc
motifStack/inst/doc/motifStack.R
motifStack/inst/doc/motifStack.Rnw
motifStack/inst/doc/motifStack.pdf
motifStack/inst/doc/motifStack_HTML.R
motifStack/inst/doc/motifStack_HTML.Rmd
motifStack/inst/doc/motifStack_HTML.html
motifStack/inst/extdata
motifStack/inst/extdata/FoxP_SOLEXA.pcm
motifStack/inst/extdata/bin_SOLEXA.pcm
motifStack/inst/extdata/cap.txt
motifStack/inst/extdata/fd64A_SOLEXA.pcm
motifStack/inst/extdata/fkh_NAR.pcm
motifStack/inst/extdata/foxo_SOLEXA.pcm
motifStack/inst/extdata/slp1_SOLEXA.pcm
motifStack/inst/extdata/slp2_SOLEXA.pcm
motifStack/inst/unitTests
motifStack/inst/unitTests/test_motifStack.R
motifStack/man
motifStack/man/DNAmotifAlignment.Rd motifStack/man/colorset.Rd motifStack/man/getRankedUniqueMotifs.Rd motifStack/man/highlightCol.Rd motifStack/man/mergeMotifs.Rd motifStack/man/motifCircos.Rd motifStack/man/motifCloud.Rd motifStack/man/motifPiles.Rd motifStack/man/motifSig-class.Rd motifStack/man/motifSig-methods.Rd motifStack/man/motifSignature.Rd motifStack/man/motifStack-package.Rd motifStack/man/motifStack.Rd motifStack/man/ouNode-class.Rd motifStack/man/pcm-class.Rd motifStack/man/pcm-methods.Rd motifStack/man/pfm-class.Rd motifStack/man/pfm-methods.Rd motifStack/man/pfm2pwm.Rd motifStack/man/plotMotifLogo.Rd motifStack/man/plotMotifLogoA.Rd motifStack/man/plotMotifLogoStack.Rd motifStack/man/plotMotifLogoStackWithTree.Rd motifStack/man/plotMotifOverMotif.Rd motifStack/man/plotMotifStackWithPhylog.Rd motifStack/man/plotMotifStackWithRadialPhylog.Rd motifStack/man/plotXaxis.Rd motifStack/man/plotYaxis.Rd motifStack/man/readPCM.Rd motifStack/man/reorderUPGMAtree.Rd
motifStack/tests
motifStack/tests/runTests.R
motifStack/vignettes
motifStack/vignettes/motifStack.Rnw
motifStack/vignettes/motifStack_HTML.Rmd
motifStack/vignettes/ref.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.