Files in jianhong/motifStack
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
DESCRIPTION
NAMESPACE
NEWS
R/AAmotifAlignment.R
R/DNAmotifAlignment.R
R/DNAmotifToRNAmotif.R
R/alignmentByPCC.R
R/browseMotifs.R
R/clusterMotifs.R
R/getRankedUniqueMotifs.R
R/globals.R
R/importMatrix.R
R/marker.R
R/matalign.R
R/mergeMotifs.R
R/motifCircos.R
R/motifCloud.R
R/motifHclust.R
R/motifPiles.R
R/motifSignature.R
R/motifStack-Package.R
R/motifStack.R
R/pcm.R
R/pfm.R
R/plotAffinityLogo.R
R/plotMotifLogo.R
R/plotMotifLogoStack.R
R/plotMotifLogoStackWithTree.R
R/plotMotifOverMotif.R
R/plotMotifStackWithPhylog.R
R/plotMotifStackWithRadialPhylog.R
R/privateUtilities.R
R/psam.R
R/pssm.R
R/publicUtilities.R
R/reorderUPGMAtree.R
R/signature.R
README.md
inst/CITATION
inst/extdata/.Rapp.history
inst/extdata/FoxP_SOLEXA.pcm
inst/extdata/MA0002.1.jaspar
inst/extdata/PSAM.mxr
inst/extdata/PWM.cisbp
inst/extdata/RUNX1.pfm
inst/extdata/RUNX1.transfac
inst/extdata/bin_SOLEXA.pcm
inst/extdata/cap.txt
inst/extdata/dna.meme
inst/extdata/fd64A_SOLEXA.pcm
inst/extdata/fkh_NAR.pcm
inst/extdata/foxo_SOLEXA.pcm
inst/extdata/momo.txt
inst/extdata/prot.meme
inst/extdata/rna.meme
inst/extdata/slp1_SOLEXA.pcm
inst/extdata/slp2.pfm
inst/extdata/slp2_SOLEXA.pcm
inst/extdata/test.beeml
inst/extdata/transfac.like.test.transfac
inst/htmlwidgets/browseMotifs.js
inst/htmlwidgets/browseMotifs.yaml
inst/htmlwidgets/lib/d3-tip/d3-tip.css
inst/htmlwidgets/lib/d3-tip/d3-tip.js
inst/htmlwidgets/lib/d3/d3.v4.min.js
inst/htmlwidgets/lib/plotWebLogo/d3-plotWebLogo.css
inst/htmlwidgets/lib/plotWebLogo/d3-plotWebLogo.js
inst/htmlwidgets/lib/saveSvgAsPng/saveSvgAsPng.js
inst/unitTests/test_motifStack.R
man/AAmotifAlignment.Rd
man/DNAmotifAlignment.Rd
man/DNAmotifToRNAmotif.Rd
man/GeomMotif.Rd
man/browseMotifs-shiny.Rd
man/browseMotifs.Rd
man/calF.Rd
man/calI.Rd
man/clusterMotifs.Rd
man/colorset.Rd
man/compare2profiles.Rd
man/compareProfiles.Rd
man/dpGlobal.Rd
man/dpLocal.Rd
man/geom_motif.Rd
man/getALLRscoreFromCounts.Rd
man/getDistance.Rd
man/getRankedUniqueMotifs.Rd
man/getScore.Rd
man/highlightCol.Rd
man/importMatrix.Rd
man/marker-class.Rd
man/matalign.Rd
man/mergeMotifs.Rd
man/motifCircos.Rd
man/motifCloud.Rd
man/motifGrob.Rd
man/motifHclust.Rd
man/motifPiles.Rd
man/motifSig-class.Rd
man/motifSignature.Rd
man/motifStack-package.Rd
man/motifStack.Rd
man/ouNode-class.Rd
man/pcm-class.Rd
man/pfm-class.Rd
man/pfm2pwm.Rd
man/plotAffinityLogo.Rd
man/plotMotifLogo.Rd
man/plotMotifLogoA.Rd
man/plotMotifLogoStack.Rd
man/plotMotifLogoStackWithTree.Rd
man/plotMotifOverMotif.Rd
man/plotMotifStackWithPhylog.Rd
man/plotMotifStackWithRadialPhylog.Rd
man/plotXaxis.Rd
man/plotYaxis.Rd
man/psam-class.Rd
man/pssm-class.Rd
man/readPCM.Rd
man/reorderUPGMAtree.Rd
man/traceBackGlobal.Rd
man/traceBackLocal.Rd
tests/runTests.R
vignettes/motifStack_HTML.Rmd
vignettes/nature.csl
vignettes/ref.bib
