DNEA
This is the development version of DNEA; for the stable release version, see DNEA.
Differential Network Enrichment Analysis for Biological Data
Bioconductor version: Development (3.24)
The DNEA R package is the latest implementation of the Differential Network Enrichment Analysis algorithm and is the successor to the Filigree Java-application described in Iyer et al. (2020). The package is designed to take as input an m x n expression matrix for some -omics modality (ie. metabolomics, lipidomics, proteomics, etc.) and jointly estimate the biological network associations of each condition using the DNEA algorithm described in Ma et al. (2019). This approach provides a framework for data-driven enrichment analysis across two experimental conditions that utilizes the underlying correlation structure of the data to determine feature-feature interactions.
Author: Christopher Patsalis [cre, aut]
, Gayatri Iyer [aut], Alla Karnovsky [fnd] (NIH_GRANT: 1U01CA235487), George Michailidis [fnd] (NIH_GRANT: 1U01CA235487)
Maintainer: Christopher Patsalis <chrispatsalis at gmail.com>
citation("DNEA")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("DNEA")
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("DNEA")| DNEA | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, DataImport, DifferentialExpression, Lipidomics, Metabolomics, Network, NetworkEnrichment, Proteomics, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.2) |
| Imports | BiocParallel, dplyr, gdata, glasso, igraph (>= 2.0.3), janitor, Matrix, methods, netgsa, stats, stringr, utils, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/Karnovsky-Lab/DNEA |
| Bug Reports | https://github.com/Karnovsky-Lab/DNEA/issues |
See More
| Suggests | BiocStyle, ggplot2, Hmisc, kableExtra, knitr, pheatmap, rmarkdown, testthat (>= 3.0.0), withr, airway |
| Linking To | |
| Enhances | massdataset |
| 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 | DNEA_1.3.0.tar.gz |
| Windows Binary (x86_64) | DNEA_1.3.0.zip |
| macOS Binary (big-sur-x86_64) | DNEA_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | DNEA_1.3.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DNEA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DNEA |
| Bioc Package Browser | https://code.bioconductor.org/browse/DNEA/ |
| Package Short Url | https://bioconductor.org/packages/DNEA/ |
| Package Downloads Report | Download Stats |