graper
This is the released version of graper; for the devel version, see graper.
Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes
Bioconductor version: Release (3.23)
This package enables regression and classification on high-dimensional data with different relative strengths of penalization for different feature groups, such as different assays or omic types. The optimal relative strengths are chosen adaptively. Optimisation is performed using a variational Bayes approach.
Author: Britta Velten [aut, cre], Wolfgang Huber [aut]
Maintainer: Britta Velten <britta.velten at gmail.com>
citation("graper")):
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")
BiocManager::install("graper")
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("graper")| example_linear | HTML | R Script |
| example_logistic | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, Classification, Regression, Software |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.6) |
| Imports | Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat |
| Linking To | Rcpp, RcppArmadillo, BH |
| 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 | graper_1.28.0.tar.gz |
| Windows Binary (x86_64) | graper_1.28.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | graper_1.28.0.tgz |
| macOS Binary (sonoma-arm64) | graper_1.28.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/graper |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/graper |
| Bioc Package Browser | https://code.bioconductor.org/browse/graper/ |
| Package Short Url | https://bioconductor.org/packages/graper/ |
| Package Downloads Report | Download Stats |