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 (3.12)

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>

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

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.13.0
In Bioconductor since BioC 3.5 (R-3.4) (3 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/
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