INDEED

DOI: 10.18129/B9.bioc.INDEED    

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 (3.11)

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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.1.0
In Bioconductor since BioC 3.8 (R-3.5) (1 year)
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_2.1.0.tar.gz
Windows Binary INDEED_2.1.0.zip
Mac OS X 10.11 (El Capitan) INDEED_2.1.0.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

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