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("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 | ||
| 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 |