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

Files in this package

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.

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