Logolas

DOI: 10.18129/B9.bioc.Logolas    

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

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

Bioconductor version: Development (3.9)

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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Logolas", version = "3.9")

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 1.7.0
In Bioconductor since BioC 3.5 (R-3.4) (1.5 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_1.7.0.tar.gz
Windows Binary Logolas_1.7.0.zip
Mac OS X 10.11 (El Capitan) Logolas_1.7.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: