Logolas

This package is for version 3.8 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see Logolas.

EDLogo Plots Featuring String Logos and Adaptive Scaling of Position-Weight Matrices

DOI: 10.18129/B9.bioc.Logolas

Bioconductor version: 3.8

Produces logo plots highlighting both enrichment and depletion of characters, allows for plotting of string symbols, and performs scaling of position-weights adaptively, along with several fun stylizations.

Author: Kushal Dey [aut, cre], Dongyue Xie [aut], Peter Carbonetto [ctb], Matthew Stephens [aut]

Maintainer: Kushal Dey <kkdey at uchicago.edu>

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

Installation

To install this package, start R (version "3.5") and enter:


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

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("Logolas")

Guided Logolas Tutorial HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Bayesian, SequenceMatching, Software, Visualization

Version 1.6.0

In Bioconductor since BioC 3.5 (R-3.4) (7 years)

License GPL (>= 2)

Depends R (>= 3.4)

Imports grid, SQUAREM, LaplacesDemon, stats, graphics, utils, ggplot2, gridBase, Biostrings

System Requirements

URL https://github.com/kkdey/Logolas

Bug Reports http://github.com/kkdey/Logolas/issues

Suggests knitr, rmarkdown, BiocStyle, Biobase, devtools, xtable, gridExtra, RColorBrewer, seqLogo, ggseqlogo

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me universalmotif

Links To Me

Build Report Build Report

Package Archives

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

Source Package Logolas_1.6.0.tar.gz

Windows Binary Logolas_1.6.0.zip

Mac OS X 10.11 (El Capitan) Logolas_1.6.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/Logolas

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Logolas

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

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

Package Downloads Report Download Stats

Old Source Packages for BioC 3.8 Source Archive