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Bioconductor - motifStack (development version)

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 (3.22)

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")

# 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")
Details biocViews Alignment, ChIPSeq, ChIPchip, DataImport, Microarray, MotifAnnotation, SequenceMatching, Sequencing, Software, Visualization Version 1.53.0 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 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 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.

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