Package: motifStack 1.57.0

Jianhong Ou

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.

Authors:Jianhong Ou, Michael Brodsky, Scot Wolfe and Lihua Julie Zhu

motifStack_1.57.0.tar.gz
motifStack_1.57.0.zip(r-4.7)motifStack_1.57.0.zip(r-4.6)motifStack_1.57.0.zip(r-4.5)
motifStack_1.57.0.tgz(r-4.6-any)motifStack_1.57.0.tgz(r-4.5-any)
motifStack_1.57.0.tar.gz(r-4.7-any)motifStack_1.57.0.tar.gz(r-4.6-any)
motifStack_1.57.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
motifStack/json (API)

# Install 'motifStack' in R:

install.packages('motifStack', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:motifStack-1.57.0(bioc 3.24)motifStack-1.56.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencematching visualization sequencing microarray alignment chipchip chipseq motifannotation dataimport

7.80 score 6 packages 235 scripts 10 mentions 47 exports 103 dependencies

Last updated from:3f6e3dc694. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	247
linux-devel-x86_64	OK	455
source / vignettes	OK	329
linux-release-x86_64	OK	427
macos-release-arm64	OK	275
macos-oldrel-arm64	OK	209
windows-devel	OK	331
windows-release	OK	315
windows-oldrel	OK	323
wasm-release	OK	197

Exports:AAmotifAlignment addBlank as.data.frame browseMotifs browseMotifsOutput clusterMotifs coerce colorset DNAmotifAlignment DNAmotifToRNAmotif format frequence geom_motif GeomMotif getIC getRankedUniqueMotifs highlightCol importMatrix matalign matrixReverseComplement mergeMotifs motifCircos motifCloud motifGrob motifHclust motifPiles motifSignature motifStack nodelist pcm2pfm pcm2pssm pfm2pwm plot plotAffinityLogo plotMotifLogo plotMotifLogoA plotMotifLogoStack plotMotifLogoStackWithTree plotMotifOverMotif plotMotifStackWithPhylog plotMotifStackWithRadialPhylog readPCM renderbrowseMotifs reorderUPGMAtree sigColor signatures trimMotif

Dependencies:abind ade4 askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome bslib cachem caTools cigarillo cli codetools cpp11 crayon curl DBI DelayedArray digest DirichletMultinomial evaluate farver fastmap fontawesome formatR fs futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 glue gtable gtools highr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite knitr labeling lambda.r lattice lifecycle MASS Matrix MatrixGenerics matrixStats memoise mime openssl pixmap pkgconfig pwalign R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl restfulr Rhtslib rjson rlang rmarkdown Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo seqLogo snow sp SparseArray SummarizedExperiment sys TFBSTools TFMPvalue tinytex vctrs viridisLite withr xfun XML XVector yaml

motifStack Vignette

Rendered frommotifStack_HTML.Rmdusingknitr::rmarkdown

Last update: 2022-04-19
Started: 2015-09-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence	motifStack-package
align AA motifs	AAmotifAlignment
browse motifs	browseMotifs
Shiny bindings for browseMotifs	browseMotifs-shiny browseMotifsOutput renderbrowseMotifs
calculate frequence	calF
calculate I'	calI
cluster motifs	clusterMotifs
retrieve color setting for logo	colorset
compare two profiles	compare2profiles
comapre w pcm	compareProfiles
align DNA motifs	DNAmotifAlignment
convert DNA motif into RNA motif	DNAmotifToRNAmotif
Global alignment version	dpGlobal
Dynamic programming function, local version	dpLocal
geom_motif	geom_motif
GeomMotif object	GeomMotif
calculate ALLR from counts	getALLRscoreFromCounts
Calculate distances between two profiles	getDistance
get the unique motif in each category grouped by distance	getRankedUniqueMotifs
Calculate pair_wise position score	getScore
add alpha transparency value to a color	highlightCol
import motifs from local files	importMatrix
Class 'marker'	$,marker-method $<-,marker-method marker marker-class
Matrix Aligner	matalign
merge multiple motifs	mergeMotifs
plot sequence logo stacks with a radial phylogenic tree and multiple color rings	motifCircos
plot a DNA sequence logo cloud	motifCloud
Motif Grob	motifGrob
Hierarchical Clustering motifs	motifHclust
plot sequence logo stacks with a linear phylogenic tree and multiple color sets	motifPiles
Class '"motifSig"'	$,motifSig-method $<-,motifSig-method frequence frequence,motifSig-method motifSig motifSig-class nodelist nodelist,motifSig-method sigColor sigColor,motifSig-method signatures signatures,motifSig-method
get signatures from motifs	motifSignature
plot a DNA sequence logo stack	motifStack
Class 'ouNode'	$,ouNode-method $<-,ouNode-method ouNode ouNode-class
Class '"pcm"'	$,pcm-method $<-,pcm-method addBlank addBlank,pcm,numeric,logical-method as as.data.frame,pcm-method coerce,pcm,matrix-method format,pcm-method getIC getIC,pcm,ANY-method matrixReverseComplement matrixReverseComplement,pcm-method pcm pcm-class pcm2pfm pcm2pfm,data.frame,ANY-method pcm2pfm,data.frame,numeric-method pcm2pfm,list,ANY-method pcm2pfm,list,numeric-method pcm2pfm,matrix,ANY-method pcm2pfm,matrix,numeric-method pcm2pfm,pcm,ANY-method pcm2pssm pcm2pssm,data.frame,ANY-method pcm2pssm,data.frame,numeric-method pcm2pssm,list,ANY-method pcm2pssm,list,numeric-method pcm2pssm,matrix,ANY-method pcm2pssm,matrix,numeric-method pcm2pssm,pcm,ANY-method plot plot,pcm,ANY-method trimMotif trimMotif,pcm,numeric-method
Class '"pfm"'	$,pfm-method $<-,pfm-method addBlank,pfm,numeric,logical-method as.data.frame,pfm-method coerce coerce,pfm,matrix-method format,pfm-method getIC,matrix,matrix-method getIC,matrix,numeric-method getIC,pfm,ANY-method matrixReverseComplement,pfm-method pfm pfm-class plot,pfm,ANY-method trimMotif,pfm,numeric-method
convert pfm object to PWM	pfm2pwm
plot affinity logo	plotAffinityLogo
plot sequence logo	plotMotifLogo
plot sequence logo without plot.new	plotMotifLogoA
plot sequence logos stack	plotMotifLogoStack
plot sequence logos stack with hierarchical cluster tree	plotMotifLogoStackWithTree
plot motif over another motif	plotMotifOverMotif
plot sequence logo stacks with a ape4-style phylogenic tree	plotMotifStackWithPhylog
plot sequence logo stacks with a radial phylogenic tree	plotMotifStackWithRadialPhylog
plot x-axis	plotXaxis
plot y-axis	plotYaxis
Class '"psam"'	$,psam-method $<-,psam-method addBlank,psam,numeric,logical-method as() as.data.frame,psam-method coerce,psam,matrix-method format,psam-method matrixReverseComplement,psam-method plot,psam,ANY-method psam psam-class
Class '"pssm"'	$,pssm-method $<-,pssm-method addBlank,pssm,numeric,logical-method as.data.frame,pssm-method coerce() coerce,pssm,matrix-method format,pssm-method matrixReverseComplement,pssm-method plot,pssm,ANY-method pssm pssm-class
read pcm from a path	readPCM
re-order UPGMA tree	reorderUPGMAtree
traceback global	traceBackGlobal
traceback local	traceBackLocal