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

AAmotifAlignmentalign AA motifs
browseMotifsbrowse motifs
browseMotifs-shinyShiny bindings for browseMotifs
calFcalculate frequence
calIcalculate I'
clusterMotifscluster motifs
colorsetretrieve color setting for logo
compare2profilescompare two profiles
compareProfilescomapre w pcm
DNAmotifAlignmentalign DNA motifs
DNAmotifToRNAmotifconvert DNA motif into RNA motif
dpGlobalGlobal alignment version
dpLocalDynamic programming function, local version
geom_motifgeom_motif
GeomMotifGeomMotif object
getALLRscoreFromCountscalculate ALLR from counts
getDistanceCalculate distances between two profiles
getRankedUniqueMotifsget the unique motif in each category grouped by distance
getScoreCalculate pair_wise position score
highlightColadd alpha transparency value to a color
importMatriximport motifs from local files
marker-classClass 'marker'
matalignMatrix Aligner
mergeMotifsmerge multiple motifs
motifCircosplot sequence logo stacks with a radial phylogenic tree and...
motifCloudplot a DNA sequence logo cloud
motifGrobMotif Grob
motifHclustHierarchical Clustering motifs
motifPilesplot sequence logo stacks with a linear phylogenic tree and...
motifSig-classClass '"motifSig"'
motifSignatureget signatures from motifs
motifStackplot a DNA sequence logo stack
motifStack-packagePlot stacked logos for single or multiple DNA, RNA and amino...
ouNode-classClass 'ouNode'
pcm-classClass '"pcm"'
pfm2pwmconvert pfm object to PWM
pfm-classClass '"pfm"'
plotAffinityLogoplot affinity logo
plotMotifLogoplot sequence logo
plotMotifLogoAplot sequence logo without plot.new
plotMotifLogoStackplot sequence logos stack
plotMotifLogoStackWithTreeplot sequence logos stack with hierarchical cluster tree
plotMotifOverMotifplot motif over another motif
plotMotifStackWithPhylogplot sequence logo stacks with a ape4-style phylogenic tree
plotMotifStackWithRadialPhylogplot sequence logo stacks with a radial phylogenic tree
plotXaxisplot x-axis
plotYaxisplot y-axis
psam-classClass '"psam"'
pssm-classClass '"pssm"'
readPCMread pcm from a path
reorderUPGMAtreere-order UPGMA tree
traceBackGlobaltraceback global
traceBackLocaltraceback local
motifStack documentation built on Nov. 8, 2020, 7:43 p.m.