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seqLogo

This is the development version of seqLogo; for the stable release version, see seqLogo.

Sequence logos for DNA sequence alignments


Bioconductor version: Development (3.20)

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>

Citation (from within R, enter citation("seqLogo")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews SequenceMatching, Software
Version 1.71.0
In Bioconductor since BioC 2.0 (R-2.5) (17 years)
License LGPL (>= 2)
Depends R (>= 4.2), methods, grid
Imports stats4, grDevices
System Requirements
URL
Bug Reports https://github.com/ivanek/seqLogo/issues
See More
Suggests knitr, BiocStyle, rmarkdown, testthat
Linking To
Enhances
Depends On Me rGADEM, generegulation
Imports Me IntEREst, PWMEnrich, RCAS, rGADEM, riboSeqR, scanMiR, SPLINTER, TFBSTools
Suggests Me BCRANK, DiffLogo, igvR, MAGAR, motifcounter, MotifDb, universalmotif, phangorn
Links To Me
Build Report Build Report

Package Archives

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

Source Package seqLogo_1.71.0.tar.gz
Windows Binary seqLogo_1.71.0.zip (64-bit only)
macOS Binary (x86_64) seqLogo_1.71.0.tgz
macOS Binary (arm64) seqLogo_1.71.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/seqLogo
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/seqLogo
Bioc Package Browser https://code.bioconductor.org/browse/seqLogo/
Package Short Url https://bioconductor.org/packages/seqLogo/
Package Downloads Report Download Stats