pareg
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This is the development version of pareg; for the stable release version, see pareg.
Pathway enrichment using a regularized regression approach
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Kim Philipp Jablonski <kim.philipp.jablonski at gmail.com>
citation("pareg")):
Installation
To install this package, start R (version "4.5") 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 |
Details
| biocViews | DifferentialExpression, GeneExpression, GraphAndNetwork, Network, NetworkEnrichment, Regression, Software, StatisticalMethod |
| Version | 1.11.1 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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 |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| 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 |
| Package Short Url | https://bioconductor.org/packages/pareg/ |
| Package Downloads Report | Download Stats |