DNEA
This is thereleased version of DNEA; for the devel version, seeDNEA.
Differential Network Enrichment Analysis for Biological Data
Bioconductor version: Release (3.22)
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]
ORCID: 0009-0003-4585-0017, Gayatri Iyer [aut], Alla Karnovsky [fnd] (NIH_GRANT: 1U01CA235487), George Michailidis [fnd] (NIH_GRANT: 1U01CA235487)
Maintainer: Christopher Patsalis <chrispatsalis at gmail.com>
citation("DNEA")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("DNEA")For older versions of R, please refer to the appropriateBioconductor 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 | 1.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| License | MIT + fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | DNEA_1.0.0.tar.gz |
| Windows Binary (x86_64) | DNEA_1.0.0.zip |
| macOS Binary (x86_64) | DNEA_1.0.0.tgz |
| macOS Binary (arm64) | DNEA_1.0.0.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 |