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motifStack
This is thereleased version of motifStack; for the devel version, seemotifStack.
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Bioconductor version: Release (3.22)
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")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("motifStack")For older versions of R, please refer to the appropriateBioconductor 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 | 1.54.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (13 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 |
| Suggests Me | ChIPpeakAnno,TFutils,trackViewer,tripr,universalmotif |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | motifStack_1.54.0.tar.gz |
| Windows Binary (x86_64) | motifStack_1.54.0.zip |
| macOS Binary (x86_64) | motifStack_1.54.0.tgz |
| macOS Binary (arm64) | motifStack_1.54.0.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 |