motifStack

This is the released version of motifStack; for the devel version, see motifStack.

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

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DOI: 10.18129/B9.bioc.motifStack

Bioconductor version: Release (3.22)

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 <jou at morgridge.org>

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

Installation

To install this package, start R (version "4.5") 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")

motifStack Vignette HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, ChIPSeq, ChIPchip, DataImport, Microarray, MotifAnnotation, SequenceMatching, Sequencing, Software, Visualization

Version 1.54.0

In Bioconductor since BioC 2.11 (R-2.15) (13 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

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

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_1.54.0.tar.gz

Windows Binary (x86_64) motifStack_1.53.0.zip (64-bit only)

macOS Binary (x86_64) motifStack_1.54.0.tgz

macOS Binary (arm64) motifStack_1.54.0.tgz

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