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 (3.21)
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")
):
Ou J, Wolfe SA, Brodsky MH, Zhu LJ (2018). “motifStack for the analysis of transcription factor binding site evolution.” Nature Methods, 15, 8-9. doi:10.1038/nmeth.4555, http://dx.doi.org/10.1038/nmeth.4555.
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")
motifStack Vignette | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Alignment, ChIPSeq, ChIPchip, DataImport, Microarray, MotifAnnotation, SequenceMatching, Sequencing, Software, Visualization |
Version | 1.51.0 |
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_1.51.0.tar.gz |
Windows Binary (x86_64) | motifStack_1.51.0.zip |
macOS Binary (x86_64) | |
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 |