Package: DEsubs
Version: 1.37.0
Date: 2017-07-23
Title: DEsubs: an R package for flexible identification of
        differentially expressed subpathways using RNA-seq expression
        experiments
Author: Aristidis G. Vrahatis and Panos Balomenos
Maintainer: Aristidis G. Vrahatis <agvrahatis@upatras.gr>, Panos
 Balomenos <balomenos@upatras.gr>
Description: 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.
Depends: R (>= 3.3), locfit
SystemRequirements:
License: GPL-3
NeedsCompilation: no
LazyLoad: yes
Imports: graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq,
        stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix,
        jsonlite, tools, DESeq2, methods
Suggests: RUnit, BiocGenerics, knitr, rmarkdown
VignetteBuilder: knitr
biocViews: SystemsBiology, GraphAndNetwork, Pathways, KEGG,
        GeneExpression, NetworkEnrichment, Network, RNASeq,
        DifferentialExpression, Normalization, ImmunoOncology
Config/pak/sysreqs: libglpk-dev make libicu-dev libxml2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:34:42 UTC
RemoteUrl: https://github.com/bioc/DEsubs
RemoteRef: HEAD
RemoteSha: 795ef9b4871c4aefd56f7b5e263ad54b53422fc4
Packaged: 2025-11-02 14:48:50 UTC; root
Built: R 4.6.0; ; 2025-11-02 14:51:24 UTC; windows
