Package: INDEED
Title: Interactive Visualization of Integrated Differential Expression
        and Differential Network Analysis for Biomarker Candidate
        Selection Package
Version: 2.26.0
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
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev git libglpk-dev make libharfbuzz-dev libgit2-dev
        libicu-dev libjpeg-dev libpng-dev libtiff-dev libuv1-dev
        libwebp-dev libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:48:25 UTC
RemoteUrl: https://github.com/bioc/INDEED
RemoteRef: RELEASE_3_23
RemoteSha: e2963e7130478e6e1bd5b1ceae7fada85b89fed4
NeedsCompilation: no
Packaged: 2026-04-29 22:24:10 UTC; root
Built: R 4.6.0; ; 2026-04-29 22:26:17 UTC; windows
