INDEED
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see INDEED.
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
Bioconductor version: 3.12
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("INDEED")):
Installation
To install this package, start R (version "4.0") 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 | R Script | |
| Reference Manual |
Details
| biocViews | BiologicalQuestion, DifferentialExpression, ImmunoOncology, MassSpectrometry, Metabolomics, ResearchField, Software, StatisticalMethod |
| Version | 2.4.0 |
| 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | INDEED_2.4.0.tar.gz |
| Windows Binary | INDEED_2.4.0.zip |
| macOS 10.13 (High Sierra) | INDEED_2.4.0.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 3.12 | Source Archive |