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("Logolas")):
Installation
To install this package, start R (version "4.0") 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
| Reference Manual |
Details
| biocViews | Alignment, Bayesian, SequenceMatching, Software, Visualization |
| Version | 1.14.0 |
| 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 | |
| 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 |
| Old Source Packages for BioC 3.12 | Source Archive |