Logolas

DOI: 10.18129/B9.bioc.Logolas    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see Logolas.

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

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>

Installation

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

if (!requireNamespace("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")

 

HTML	R Script	Guided Logolas Tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Bayesian, SequenceMatching, Software, Visualization
Version	1.6.0
In Bioconductor since	BioC 3.5 (R-3.4) (2 years)
License	GPL (>= 2)
Depends	R (>= 3.4)
Imports	grid, SQUAREM, LaplacesDemon, stats, graphics, utils, ggplot2, gridBase, Biostrings
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, Biobase, devtools, xtable, gridExtra, RColorBrewer, seqLogo, ggseqlogo
SystemRequirements
Enhances
URL	https://github.com/kkdey/Logolas
BugReports	http://github.com/kkdey/Logolas/issues
Depends On Me
Imports Me
Suggests Me	universalmotif
Links To Me
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
Package Short Url	http://bioconductor.org/packages/Logolas/
Package Downloads Report	Download Stats