INDEED

DOI: 10.18129/B9.bioc.INDEED    

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

Bioconductor version: Release (3.11)

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	BiologicalQuestion, DifferentialExpression, ImmunoOncology, MassSpectrometry, Metabolomics, ResearchField, Software, StatisticalMethod
Version	2.2.0
In Bioconductor since	BioC 3.8 (R-3.5) (2 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)
LinkingTo
Suggests	knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0)
SystemRequirements
Enhances
URL	http://github.com/ressomlab/INDEED
BugReports	http://github.com/ressomlab/INDEED/issues
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_2.2.0.tar.gz
Windows Binary	INDEED_2.2.0.zip
macOS 10.13 (High Sierra)	INDEED_2.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/INDEED
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/INDEED
Package Short Url	https://bioconductor.org/packages/INDEED/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive