pareg
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see pareg.
Pathway enrichment using a regularized regression approach
Bioconductor version: 3.16
Compute pathway enrichment scores while accounting for term-term relations. This package uses a regularized multiple linear regression to regress differential expression p-values obtained from multi-condition experiments on a pathway membership matrix. By doing so, it is able to incorporate additional biological knowledge into the enrichment analysis and to estimate pathway enrichment scores more robustly.
Author: Kim Philipp Jablonski [aut, cre] 
Maintainer: Kim Philipp Jablonski <kim.philipp.jablonski at gmail.com>
citation("pareg")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pareg")
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("pareg")| Get started | HTML | R Script |
| Pathway similarities | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GraphAndNetwork, Network, NetworkEnrichment, Regression, Software, StatisticalMethod |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2 years) |
| License | GPL-3 |
| Depends | R (>= 4.2), tensorflow (>= 2.2.0), tfprobability (>= 0.10.0) |
| Imports | stats, tidyr, purrr, furrr, tibble, glue, tidygraph, igraph, proxy, dplyr, magrittr, ggplot2, ggraph, rlang, progress, Matrix, matrixLaplacian, keras, nloptr, shadowtext, methods, DOSE, stringr, reticulate |
| System Requirements | |
| URL | https://github.com/cbg-ethz/pareg |
| Bug Reports | https://github.com/cbg-ethz/pareg/issues |
See More
| Suggests | knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, devtools, plotROC, PRROC, mgsa, topGO, msigdbr, betareg, fgsea, ComplexHeatmap, GGally, ggsignif, circlize, enrichplot, ggnewscale, tidyverse, cowplot, ggfittext |
| 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 | pareg_1.2.0.tar.gz |
| Windows Binary | pareg_1.2.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/pareg |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/pareg |
| Bioc Package Browser | https://code.bioconductor.org/browse/pareg/ |
| Package Short Url | https://bioconductor.org/packages/pareg/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |