INDEED

DOI: 10.18129/B9.bioc.INDEED    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see INDEED.

An Implementation of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection

Bioconductor version: 3.9

An Implementation of Integrated Differential Expression and Differential Network Analysis of Omic Data. The differential network is obtained based on partial correlation or correlation.

Author: Zhenzhi Li <zzrickli at gmail.com>

Maintainer: Zhenzhi Li <zzrickli at gmail.com>, Yiming Zuo <yimingzuo at gmail.com>

Installation

To install this package, start R (version "3.6") 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")

 

HTML	R Script	INDEED R package for cancer biomarker candidate selection
PDF		Reference Manual

Details

biocViews	BiologicalQuestion, DifferentialExpression, ImmunoOncology, MassSpectrometry, Metabolomics, ResearchField, Software, StatisticalMethod
Version	1.2.0
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
License	Artistic-2.0
Depends	R (>= 3.5), glasso (>= 1.8)
Imports	utils (>= 3.3.1), stats (>= 3.3.1), graphics (>= 3.3.1), devtools (>= 1.13.0)
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_1.2.0.tar.gz
Windows Binary	INDEED_1.2.0.zip
Mac OS X 10.11 (El Capitan)	INDEED_1.2.0.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