pareg

DOI: 10.18129/B9.bioc.pareg  

This is the development version of pareg; for the stable release version, see pareg.

Pathway enrichment using a regularized regression approach

Bioconductor version: Development (3.18)

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 (from within R, enter citation("pareg")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.5.1
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_1.5.1.tar.gz
Windows Binary pareg_1.5.1.zip
macOS Binary (x86_64) pareg_1.5.1.tgz
macOS Binary (arm64) pareg_1.5.1.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: