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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
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see LedPred.
Learning from DNA to Predict Enhancers
Bioconductor version: 3.3
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")
| R Script | LedPred Example | |
| Reference Manual | ||
| Text | NEWS | |
| Text | LICENSE |
Details
| biocViews | ChIPSeq, Classification, MotifAnnotation, Sequencing, Software, SupportVectorMachine |
| Version | 1.6.1 |
| In Bioconductor since | BioC 3.2 (R-3.2) (1 year) |
| 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.
| Package Source | LedPred_1.6.1.tar.gz |
| Windows Binary | LedPred_1.6.1.zip |
| Mac OS X 10.9 (Mavericks) | LedPred_1.6.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/LedPred/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/LedPred/ |
| Package Downloads Report | Download Stats |
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