LedPred
Learning from DNA to Predict Enhancers
Bioconductor version: Release (3.20)
This package aims at creating a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, next-generation sequencing (NGS) peaks and signals and other numerical scores of the sequences using supervised classification. The package contains a workflow based on the support vector machine (SVM) algorithm that maps features to sequences, optimize SVM parameters and feature number and creates a model that can be stored and used to score the regulatory potential of unknown sequences.
Author: Elodie Darbo, Denis Seyres, Aitor Gonzalez
Maintainer: Aitor Gonzalez <aitor.gonzalez at univ-amu.fr>
citation("LedPred")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("LedPred")
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("LedPred")| LedPred Example | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ChIPSeq, Classification, MotifAnnotation, Sequencing, Software, SupportVectorMachine |
| Version | 1.40.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (9 years) |
| License | MIT | file LICENSE |
| Depends | R (>= 3.2.0), e1071 (>= 1.6) |
| Imports | akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl, ROCR, testthat |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/aitgon/LedPred/issues |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | LedPred_1.40.0.tar.gz |
| Windows Binary (x86_64) | LedPred_1.40.0.zip |
| macOS Binary (x86_64) | LedPred_1.40.0.tgz |
| macOS Binary (arm64) | LedPred_1.40.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/LedPred |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/LedPred |
| Bioc Package Browser | https://code.bioconductor.org/browse/LedPred/ |
| Package Short Url | https://bioconductor.org/packages/LedPred/ |
| Package Downloads Report | Download Stats |