LedPred

DOI: 10.18129/B9.bioc.LedPred    

Learning from DNA to Predict Enhancers

Bioconductor version: Release (3.11)

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>

Installation

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

if (!requireNamespace("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")

 

PDF	R Script	LedPred Example
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ChIPSeq, Classification, MotifAnnotation, Sequencing, Software, SupportVectorMachine
Version	1.22.0
In Bioconductor since	BioC 3.2 (R-3.2) (5 years)
License	MIT | file LICENSE
Depends	R (>= 3.2.0), e1071 (>= 1.6)
Imports	akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl, ROCR, testthat
LinkingTo
Suggests
SystemRequirements
Enhances
URL
BugReports	https://github.com/aitgon/LedPred/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	LedPred_1.22.0.tar.gz
Windows Binary	LedPred_1.22.0.zip
macOS 10.13 (High Sierra)	LedPred_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/LedPred
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/LedPred
Package Short Url	https://bioconductor.org/packages/LedPred/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive