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LedPred

Learning from DNA to Predict Enhancers

Bioconductor version: Release (3.17)

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 1.34.0
In Bioconductor since BioC 3.2 (R-3.2) (8 years)
License MIT | file LICENSE
Depends R (>= 3.2.0), e1071 (>= 1.6)
Imports akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl, ROCR, testthat
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Bug Reports https://github.com/aitgon/LedPred/issues
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Package Archives

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

Source Package LedPred_1.34.0.tar.gz
Windows Binary LedPred_1.34.0.zip (64-bit only)
macOS Binary (x86_64) LedPred_1.34.0.tgz
macOS Binary (arm64) LedPred_1.34.0.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