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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 (3.19)

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 "4.4") 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")
Get started HTML R Script
Pathway similarities HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, Network, NetworkEnrichment, Regression, Software, StatisticalMethod
Version 1.7.0
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, 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
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, 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
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Package Archives

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

Source Package pareg_1.7.0.tar.gz
Windows Binary pareg_1.7.0.zip (64-bit only)
macOS Binary (x86_64) pareg_1.7.0.tgz
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