LedPred
This is the development version of LedPred; for the stable release version, see LedPred.
Learning from DNA to Predict Enhancers
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| LedPred Example | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ChIPSeq, Classification, MotifAnnotation, Sequencing, Software, SupportVectorMachine |
| Version | 1.47.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 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_1.47.0.tar.gz |
| Windows Binary (x86_64) | LedPred_1.47.0.zip |
| macOS Binary (big-sur-x86_64) | LedPred_1.47.0.tgz |
| macOS Binary (sonoma-arm64) | LedPred_1.47.0.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 |