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motifStack

This is the development version of motifStack; for the stable release version, see motifStack.

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


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
motifStack Vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, ChIPSeq, ChIPchip, DataImport, Microarray, MotifAnnotation, SequenceMatching, Sequencing, Software, Visualization
Version 1.47.1
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License GPL (>= 2)
Depends R (>= 2.15.1), methods, grid
Imports ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets, stats, stats4, utils, XML, TFBSTools
System Requirements
URL
See More
Suggests Cairo, grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020
Linking To
Enhances
Depends On Me generegulation
Imports Me ATACseqQC, atSNP, dagLogo, motifbreakR, ribosomeProfilingQC, TCGAWorkflow
Suggests Me ChIPpeakAnno, TFutils, trackViewer, tripr, universalmotif
Links To Me
Build Report Build Report

Package Archives

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

Source Package motifStack_1.47.1.tar.gz
Windows Binary motifStack_1.47.1.zip
macOS Binary (x86_64) motifStack_1.47.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/motifStack
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/motifStack
Bioc Package Browser https://code.bioconductor.org/browse/motifStack/
Package Short Url https://bioconductor.org/packages/motifStack/
Package Downloads Report Download Stats