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


Reference Manual	PDF

Details

biocViews	DifferentialExpression, GeneExpression, GraphAndNetwork, Network, NetworkEnrichment, Regression, Software, StatisticalMethod
Version	1.5.0
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, furrr, tibble, glue, tidygraph, igraph, proxy, dplyr, magrittr, ggplot2, ggraph, rlang, progress, Matrix, matrixLaplacian, keras, nloptr, shadowtext, methods, DOSE, stringr, reticulate
Linking To
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
System Requirements
Enhances
URL	https://github.com/cbg-ethz/pareg
Bug Reports	https://github.com/cbg-ethz/pareg/issues

Depends On Me
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Build Report

Package Archives

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

Source Package
Windows Binary	pareg_1.5.0.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