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motifStack

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

Bioconductor version: 3.23 · Package version: 1.56.0

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.

Installation

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

BiocManager::install("motifStack")

Details

MaintainerJianhong Ou <jou@morgridge.org>
AuthorJianhong Ou, Michael Brodsky, Scot Wolfe and Lihua Julie Zhu
LicenseGPL (>= 2)
Downloads rank1155
Source branchRELEASE_3_23
biocViewsAlignment, ChIPSeq, ChIPchip, DataImport, Microarray, MotifAnnotation, SequenceMatching, Sequencing, Software, Visualization

Documentation

Download

Dependencies

Depends: R (>= 2.15.1), methods, grid

Imports: ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets, stats, stats4, utils, XML, TFBSTools

Suggests: Cairo, grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020

Reverse dependencies

Depends On Me (1): generegulation

Imports Me (5): ATACseqQC, atSNP, dagLogo, motifbreakR, ribosomeProfilingQC

Suggests Me (5): ChIPpeakAnno, TFutils, trackViewer, tripr, universalmotif