INDEED
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
Bioconductor version: 3.24 · Package version: 2.27.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("INDEED")Details
| Maintainer | Ressom group <hwr@georgetown.edu>, Yiming Zuo <yimingzuo@gmail.com> |
| Author | Yiming Zuo <yimingzuo@gmail.com>, Kian Ghaffari <kg.ghaffari@gmail.com>, Zhenzhi Li <zzrickli@gmail.com> |
| License | Artistic-2.0 |
| URL | http://github.com/ressomlab/INDEED |
| Bug Reports | http://github.com/ressomlab/INDEED/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | BiologicalQuestion, DifferentialExpression, ImmunoOncology, MassSpectrometry, Metabolomics, ResearchField, Software, StatisticalMethod |
| Package Short Url | https://bioconductor.org/packages/INDEED/ |
Citation
From within R, enter citation("INDEED"):
Yiming Zuo, Kian Ghaffari, Zhenzhi Li. INDEED: Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package. doi:10.18129/B9.bioc.INDEED, R package version 2.27.0, https://bioconductor.org/packages/INDEED.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | INDEED_2.27.0.tar.gz |
| Windows binary (x86_64) | INDEED_2.27.0.zip |
| macOS binary (arm64) | INDEED_2.27.0.tgz |
| macOS binary (x86_64) | INDEED_2.27.0.tgz |
Dependencies
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)
Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0)