seqLogo

This is the released version of seqLogo; for the devel version, see seqLogo.

Sequence logos for DNA sequence alignments

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DOI: 10.18129/B9.bioc.seqLogo

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0002-8403-056X

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

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

Installation

To install this package, start R (version "4.5") 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 1.76.0

In Bioconductor since BioC 2.0 (R-2.5) (18.5 years)

License LGPL (>= 2)

Depends R (>= 4.2), 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

Imports Me IntEREst, PWMEnrich, RCAS, riboSeqR, scanMiR, SPLINTER, TENET, TFBSTools, kmeRtone

Suggests Me BCRANK, DiffLogo, igvR, MAGAR, motifcounter, MotifDb, PMScanR, universalmotif

Links To Me

Build Report Build Report

Package Archives

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

Source Package seqLogo_1.76.0.tar.gz

Windows Binary (x86_64) seqLogo_1.75.0.zip (64-bit only)

macOS Binary (x86_64) seqLogo_1.76.0.tgz

macOS Binary (arm64) seqLogo_1.76.0.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