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INDEED

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


Bioconductor version: Release (3.18)

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 gmail.com>, Kian Ghaffari <kg.ghaffari at gmail.com>, Zhenzhi Li <zzrickli at gmail.com>

Maintainer: Ressom group <hwr at georgetown.edu>, Yiming Zuo <yimingzuo at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("INDEED")

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

Documentation

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

browseVignettes("INDEED")
INDEED R package for cancer biomarker discovery PDF R Script
Reference Manual PDF

Details

biocViews BiologicalQuestion, DifferentialExpression, ImmunoOncology, MassSpectrometry, Metabolomics, ResearchField, Software, StatisticalMethod
Version 2.16.0
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)
System Requirements
URL http://github.com/ressomlab/INDEED
Bug Reports http://github.com/ressomlab/INDEED/issues
See More
Suggests knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0)
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Package Archives

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

Source Package INDEED_2.16.0.tar.gz
Windows Binary INDEED_2.16.0.zip
macOS Binary (x86_64) INDEED_2.16.0.tgz
macOS Binary (arm64) INDEED_2.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/INDEED
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/INDEED
Bioc Package Browser https://code.bioconductor.org/browse/INDEED/
Package Short Url https://bioconductor.org/packages/INDEED/
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