motifStack
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see motifStack.
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Bioconductor version: 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("motifStack")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, ChIPSeq, ChIPchip, DataImport, Microarray, MotifAnnotation, SequenceMatching, Sequencing, Software, Visualization |
| Version | 1.48.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (12 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_1.48.0.tar.gz |
| Windows Binary (x86_64) | motifStack_1.48.0.zip |
| macOS Binary (x86_64) | motifStack_1.48.0.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 |