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>

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


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

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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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
Suggests knitr, rmarkdown, BiocStyle, Biobase, devtools, xtable, gridExtra, RColorBrewer, seqLogo, ggseqlogo
URL https://github.com/kkdey/Logolas
BugReports http://github.com/kkdey/Logolas/issues
Depends On Me
Imports Me
Suggests Me universalmotif
Links To Me
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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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