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DEsubs

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments


Bioconductor version: Release (3.18)

DEsubs is a network-based systems biology package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customizable framework covering a broad range of operation modes at all stages of the subpathway analysis, enabling a case-specific approach. The operation modes refer to the pathway network construction and processing, the subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features. Its capabilities render it a tool-guide for both the modeler and experimentalist for the identification of more robust systems-level biomarkers for complex diseases.

Author: Aristidis G. Vrahatis and Panos Balomenos

Maintainer: Aristidis G. Vrahatis <agvrahatis at upatras.gr>, Panos Balomenos <balomenos at upatras.gr>

Citation (from within R, enter citation("DEsubs")):

Installation

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


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

BiocManager::install("DEsubs")

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("DEsubs")
DEsubs PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, ImmunoOncology, KEGG, Network, NetworkEnrichment, Normalization, Pathways, RNASeq, Software, SystemsBiology
Version 1.28.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL-3
Depends R (>= 3.3), locfit
Imports graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq, stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix, jsonlite, tools, DESeq2, methods
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Suggests RUnit, BiocGenerics, knitr, rmarkdown
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Package Archives

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

Source Package DEsubs_1.28.0.tar.gz
Windows Binary DEsubs_1.28.0.zip
macOS Binary (x86_64) DEsubs_1.28.0.tgz
macOS Binary (arm64) DEsubs_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DEsubs
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DEsubs
Bioc Package Browser https://code.bioconductor.org/browse/DEsubs/
Package Short Url https://bioconductor.org/packages/DEsubs/
Package Downloads Report Download Stats