Logolas

This package is for version 3.9 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


Bioconductor version: 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 (version "3.6") 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

Details

biocViews Alignment, Bayesian, SequenceMatching, Software, Visualization
Version 1.8.0
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
See More
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_1.8.0.tar.gz
Windows Binary Logolas_1.8.0.zip
Mac OS X 10.11 (El Capitan) Logolas_1.8.0.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 3.9 Source Archive