Logolas

DOI: 10.18129/B9.bioc.Logolas    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 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: 3.12

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 <kkdey at uchicago.edu>, Dongyue Xie <kkdey at uchicago.edu>, Peter Carbonetto <kkdey at uchicago.edu>, Matthew Stephens <kkdey at uchicago.edu>

Maintainer: Kushal Dey <kkdey at uchicago.edu>

Installation

To install this package, start R (version "4.0") 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

PDF		Reference Manual

Details

biocViews	Alignment, Bayesian, SequenceMatching, Software, Visualization
Version	1.14.0
In Bioconductor since	BioC 3.5 (R-3.4) (4 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
Windows Binary
macOS 10.13 (High Sierra)
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	https://bioconductor.org/packages/Logolas/
Package Downloads Report	Download Stats