Package: DEsubs

 Version: 1.20.0

 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
 Repository: Bioconductor
 Date/Publication:
 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