LedPred
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see LedPred.
Learning from DNA to Predict Enhancers
Bioconductor version: 3.7
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("LedPred")
):
Installation
To install this package, start R (version "3.5") 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 | R Script | |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | ChIPSeq, Classification, MotifAnnotation, Sequencing, Software, SupportVectorMachine |
Version | 1.14.1 |
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 | |
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Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | LedPred_1.14.1.tar.gz |
Windows Binary | LedPred_1.14.1.zip |
Mac OS X 10.11 (El Capitan) | LedPred_1.14.1.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 |
Old Source Packages for BioC 3.7 | Source Archive |