seqLogo

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see seqLogo.

Sequence logos for DNA sequence alignments

Bioconductor version: 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>

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

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")

Sequence logos for DNA sequence alignments HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews SequenceMatching, Software

Version 1.60.0

In Bioconductor since BioC 2.0 (R-2.5) (17 years)

License LGPL (>= 2)

Depends methods, grid

Imports stats4, grDevices

System Requirements

URL

Bug Reports https://github.com/ivanek/seqLogo/issues

Suggests knitr, BiocStyle, rmarkdown, testthat

Linking To

Enhances

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 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

Bioc Package Browser https://code.bioconductor.org/browse/seqLogo/

Package Short Url https://bioconductor.org/packages/seqLogo/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.14 Source Archive