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This is the development version of INDEED; for the stable release version, see INDEED.

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package

Bioconductor version: Development (3.20)

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.

Author: Yiming Zuo <yimingzuo at>, Kian Ghaffari <kg.ghaffari at>, Zhenzhi Li <zzrickli at>

Maintainer: Ressom group <hwr at>, Yiming Zuo <yimingzuo at>

Citation (from within R, enter citation("INDEED")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

INDEED R package for cancer biomarker discovery PDF R Script
Reference Manual PDF


biocViews BiologicalQuestion, DifferentialExpression, ImmunoOncology, MassSpectrometry, Metabolomics, ResearchField, Software, StatisticalMethod
Version 2.19.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License Artistic-2.0
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)
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Suggests knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package INDEED_2.19.0.tar.gz
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macOS Binary (arm64) INDEED_2.19.0.tgz
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