To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("LedPred")

In most cases, you don't need to download the package archive at all.

LedPred

DOI: 10.18129/B9.bioc.LedPred    

Learning from DNA to Predict Enhancers

Bioconductor version: Release (3.6)

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 (from within R, enter citation("LedPred")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("LedPred")

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 1.12.0
In Bioconductor since BioC 3.2 (R-3.2) (2 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
Build Report  

Package Archives

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

Source Package LedPred_1.12.0.tar.gz
Windows Binary LedPred_1.12.0.zip
Mac OS X 10.11 (El Capitan) LedPred_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/LedPred
Package Short Url http://bioconductor.org/packages/LedPred/
Package Downloads Report Download Stats

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