motifStack
This package is for version 3.11 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: 3.11
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 "4.0") 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 | 1.32.1 |
| In Bioconductor since | BioC 2.11 (R-2.15) (11.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.15.1), methods, grImport2, grid, MotIV, ade4, Biostrings |
| Imports | XML, scales, htmlwidgets, grDevices, stats, stats4, graphics, utils, ggplot2 |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr, httr, htmltools |
| Linking To | |
| Enhances | |
| Depends On Me | generegulation |
| Imports Me | ATACseqQC, atSNP, dagLogo, LowMACA, motifbreakR, ribosomeProfilingQC, TCGAWorkflow |
| Suggests Me | ChIPpeakAnno, TFutils, universalmotif |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | motifStack_1.32.1.tar.gz |
| Windows Binary | motifStack_1.32.1.zip |
| macOS 10.13 (High Sierra) | motifStack_1.32.1.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 |
| Old Source Packages for BioC 3.11 | Source Archive |