Package: INDEED
Title: Interactive Visualization of Integrated Differential Expression
        and Differential Network Analysis for Biomarker Candidate
        Selection Package
Version: 2.24.0
Author: Yiming Zuo <yimingzuo@gmail.com>, Kian Ghaffari <kg.ghaffari@gmail.com>, Zhenzhi Li <zzrickli@gmail.com>
Maintainer: Ressom group <hwr@georgetown.edu>,
 Yiming Zuo <yimingzuo@gmail.com>
Description: An R package for integrated differential expression and differential network analysis based on omic data for cancer biomarker discovery. Both correlation and partial correlation can be used to generate differential network to aid the traditional differential expression analysis to identify changes between biomolecules on both their expression and pairwise association levels. A detailed description of the methodology has been published in Methods journal (PMID: 27592383). An interactive visualization feature allows for the exploration and selection of candidate biomarkers. 
License: Artistic-2.0
URL: http://github.com/ressomlab/INDEED
BugReports: http://github.com/ressomlab/INDEED/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends: glasso (>= 1.8), R (>= 3.5)
Imports: devtools (>= 1.13.0), graphics (>= 3.3.1), stats (>= 3.3.1),
        utils (>= 3.3.1), igraph (>= 1.2.4), visNetwork(>= 2.0.6)
Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0)
VignetteBuilder: knitr
biocViews: ImmunoOncology, Software, ResearchField, BiologicalQuestion,
        StatisticalMethod, DifferentialExpression, MassSpectrometry,
        Metabolomics
git_url: https://git.bioconductor.org/packages/INDEED
git_branch: RELEASE_3_22
git_last_commit: 00316e6
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 03:08:48 UTC; biocbuild
Built: R 4.5.1; ; 2025-10-30 09:28:19 UTC; unix
