Package: INDEED Title: Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package Version: 2.27.0 Author: Yiming Zuo , Kian Ghaffari , Zhenzhi Li Maintainer: Ressom group , Yiming Zuo 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.r-universe.dev Date/Publication: 2026-04-28 12:48:25 UTC RemoteUrl: https://github.com/bioc/INDEED RemoteRef: HEAD RemoteSha: 094b45e07c179daff1a0729dd0cba95efe3e6764 NeedsCompilation: no Packaged: 2026-07-08 05:35:55 UTC; root