seqLogo

DOI: 10.18129/B9.bioc.seqLogo    

Sequence logos for DNA sequence alignments

Bioconductor version: Release (3.14)

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

Author: Oliver Bembom [aut], Robert Ivanek [aut, cre]

Maintainer: Robert Ivanek <robert.ivanek at unibas.ch>

Installation

To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("seqLogo")

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("seqLogo")

 

HTML	R Script	Sequence logos for DNA sequence alignments
PDF		Reference Manual
Text		NEWS

Details

biocViews	SequenceMatching, Software
Version	1.60.0
In Bioconductor since	BioC 2.0 (R-2.5) (15 years)
License	LGPL (>= 2)
Depends	methods, grid
Imports	stats4, grDevices
LinkingTo
Suggests	knitr, BiocStyle, rmarkdown, testthat
SystemRequirements
Enhances
URL
BugReports	https://github.com/ivanek/seqLogo/issues
Depends On Me	generegulation, rGADEM
Imports Me	igvR, IntEREst, PWMEnrich, rGADEM, riboSeqR, scanMiR, SPLINTER, TFBSTools
Suggests Me	BCRANK, DiffLogo, MAGAR, motifcounter, MotifDb, universalmotif
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	seqLogo_1.60.0.tar.gz
Windows Binary	seqLogo_1.60.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	seqLogo_1.60.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/seqLogo
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/seqLogo
Package Short Url	https://bioconductor.org/packages/seqLogo/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive