motifStack

DOI: 10.18129/B9.bioc.motifStack    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see motifStack.

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

Bioconductor version: 3.15

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.

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

Maintainer: Jianhong Ou <jianhong.ou at duke.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("motifStack")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("motifStack")

 

HTML	R Script	motifStack Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, ChIPSeq, ChIPchip, DataImport, Microarray, MotifAnnotation, SequenceMatching, Sequencing, Software, Visualization
Version	1.40.0
In Bioconductor since	BioC 2.11 (R-2.15) (10 years)
License	GPL (>= 2)
Depends	R (>= 2.15.1), methods, grid
Imports	ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets, stats, stats4, utils, XML, TFBSTools
LinkingTo
Suggests	grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020
SystemRequirements
Enhances
URL
Depends On Me	generegulation
Imports Me	ATACseqQC, atSNP, dagLogo, LowMACA, motifbreakR, ribosomeProfilingQC, TCGAWorkflow
Suggests Me	ChIPpeakAnno, TFutils, tripr, universalmotif
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	motifStack_1.40.0.tar.gz
Windows Binary	motifStack_1.40.0.zip
macOS Binary (x86_64)	motifStack_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/motifStack
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/motifStack
Package Short Url	https://bioconductor.org/packages/motifStack/
Package Downloads Report	Download Stats