Welcome to the new bioconductor.org!

LedPred

Learning from DNA to Predict Enhancers


Bioconductor version: Release (3.18)

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 (version "4.3") 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 PDF R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews ChIPSeq, Classification, MotifAnnotation, Sequencing, Software, SupportVectorMachine
Version 1.36.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License MIT | file LICENSE
Depends R (>= 3.2.0), e1071 (>= 1.6)
Imports akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl, ROCR, testthat
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_1.36.0.tar.gz
Windows Binary LedPred_1.36.0.zip
macOS Binary (x86_64) LedPred_1.36.0.tgz
macOS Binary (arm64) LedPred_1.36.0.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