DOI: 10.18129/B9.bioc.pareg  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see pareg.

Pathway enrichment using a regularized regression approach

Bioconductor version: 3.16

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>

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biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, Network, NetworkEnrichment, Regression, Software, StatisticalMethod
Version 1.2.0
In Bioconductor since BioC 3.15 (R-4.2) (1 year)
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
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
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