motifStack

DOI: 10.18129/B9.bioc.motifStack    

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

Bioconductor version: Release (3.6)

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 umassmed.edu>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("motifStack")

Documentation

HTML	R Script	motifStack Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, ChIPSeq, ChIPchip, DataImport, Microarray, MotifAnnotation, SequenceMatching, Sequencing, Software, Visualization
Version	1.22.4
In Bioconductor since	BioC 2.11 (R-2.15) (5.5 years)
License	GPL (>= 2)
Depends	R (>= 2.15.1), methods, grImport, grid, MotIV, ade4, Biostrings
Imports	XML, scales, htmlwidgets, grDevices, stats, utils
LinkingTo
Suggests	RUnit, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me	dagLogo
Imports Me	ATACseqQC, LowMACA, motifbreakR
Suggests Me	ChIPpeakAnno
Build Report

Package Archives

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

Source Package	motifStack_1.22.4.tar.gz
Windows Binary	motifStack_1.22.4.zip
Mac OS X 10.11 (El Capitan)	motifStack_1.22.4.tgz
Source Repository	git clone https://git.bioconductor.org/packages/motifStack
Package Short Url	http://bioconductor.org/packages/motifStack/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive