pareg

DOI: 10.18129/B9.bioc.pareg  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see pareg.

Pathway enrichment using a regularized regression approach

Bioconductor version: 3.17

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 "4.3") 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	1.4.1
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 years)
License	GPL-3
Depends	R (>= 4.2), tensorflow (>= 2.2.0), tfprobability (>= 0.10.0)
Imports	stats, tidyr, purrr, future, doFuture, foreach, doRNG, tibble, glue, tidygraph, igraph, proxy, dplyr, magrittr, ggplot2, ggraph, rlang, progress, Matrix, keras, nloptr, ggrepel, methods, DOSE, stringr, reticulate, logger, hms, devtools, basilisk
LinkingTo
Suggests	knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR, plotROC, PRROC, mgsa, topGO, msigdbr, betareg, fgsea, ComplexHeatmap, GGally, ggsignif, circlize, enrichplot, ggnewscale, tidyverse, cowplot, ggfittext, simplifyEnrichment, GSEABenchmarkeR, BiocParallel, ggupset, latex2exp, org.Hs.eg.db, GO.db
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_1.4.1.tar.gz
Windows Binary	pareg_1.4.1.zip
macOS Binary (x86_64)	pareg_1.4.1.tgz
macOS Binary (arm64)	pareg_1.4.1.tgz
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