DOI: 10.18129/B9.bioc.INDEED  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see INDEED.

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

Bioconductor version: 3.17

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 "4.3") and enter:

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


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:



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


biocViews BiologicalQuestion, DifferentialExpression, ImmunoOncology, MassSpectrometry, Metabolomics, ResearchField, Software, StatisticalMethod
Version 2.14.0
In Bioconductor since BioC 3.8 (R-3.5) (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)
Suggests knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0)
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package INDEED_2.14.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) INDEED_2.14.0.tgz
macOS Binary (arm64) INDEED_2.14.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: