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Bioconductor - LedPred (development version)

LedPred

This is the development version of LedPred; for the stable release version, see LedPred.

Learning from DNA to Predict Enhancers

Bioconductor version: Development (3.22)

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 "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews ChIPSeq, Classification, MotifAnnotation, Sequencing, Software, SupportVectorMachine Version 1.43.0 In Bioconductor since BioC 3.2 (R-3.2) (9.5 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.


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