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>

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

Installation

To install this package, start R (version "3.6") 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 candidate selection HTML R Script
Reference Manual PDF

Details

biocViews BiologicalQuestion, DifferentialExpression, ImmunoOncology, MassSpectrometry, Metabolomics, ResearchField, Software, StatisticalMethod
Version 1.2.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
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)
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)
Linking To
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Build Report 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
Bioc Package Browser https://code.bioconductor.org/browse/INDEED/
Package Short Url https://bioconductor.org/packages/INDEED/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive