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 (3.24)
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("motifStack")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.57.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (14 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, 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.
| Source Package | motifStack_1.57.0.tar.gz |
| Windows Binary (x86_64) | motifStack_1.57.0.zip |
| macOS Binary (big-sur-x86_64) | motifStack_1.57.0.tgz |
| macOS Binary (sonoma-arm64) | motifStack_1.57.0.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 |