pareg

DOI: 10.18129/B9.bioc.pareg    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see pareg.

Pathway enrichment using a regularized regression approach

Bioconductor version: 3.15

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>

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")

 

HTML	R Script	Get started
HTML	R Script	Pathway similarities
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, GraphAndNetwork, Network, NetworkEnrichment, Regression, Software, StatisticalMethod
Version	1.0.0
In Bioconductor since	BioC 3.15 (R-4.2) (0.5 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
LinkingTo
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
SystemRequirements
Enhances
URL	https://github.com/cbg-ethz/pareg
BugReports	https://github.com/cbg-ethz/pareg/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	pareg_1.0.0.tar.gz
Windows Binary	pareg_1.0.0.zip
macOS Binary (x86_64)	pareg_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/pareg
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/pareg
Package Short Url	https://bioconductor.org/packages/pareg/
Package Downloads Report	Download Stats