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>

Citation (from within R, enter citation("motifStack")):

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

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