cogena
This is the development version of cogena; for the stable release version, see cogena.
co-expressed gene-set enrichment analysis
Bioconductor version: Development (3.24)
cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.
Author: Zhilong Jia [aut, cre], Michael Barnes [aut]
Maintainer: Zhilong Jia <zhilongjia at gmail.com>
citation("cogena")):
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("cogena")
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("cogena")| a workflow of cogena | R Script | |
| cogena, a workflow for gene set enrichment analysis of co-expressed genes | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, DataImport, DataRepresentation, GO, GeneExpression, GeneSetEnrichment, KEGG, Microarray, Pathways, Sequencing, Software, SystemsBiology, Visualization |
| Version | 1.47.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 years) |
| License | LGPL-3 |
| Depends | R (>= 3.6), cluster, ggplot2, kohonen |
| Imports | methods, class, gplots, mclust, amap, apcluster, foreach, parallel, doParallel, fastcluster, corrplot, biwt, Biobase, reshape2, stringr, tibble, tidyr, dplyr, devtools |
| System Requirements | |
| URL | https://github.com/zhilongjia/cogena |
| Bug Reports | https://github.com/zhilongjia/cogena/issues |
See More
| Suggests | knitr, rmarkdown (>= 2.1) |
| 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 | cogena_1.47.0.tar.gz |
| Windows Binary (x86_64) | cogena_1.47.0.zip |
| macOS Binary (big-sur-x86_64) | cogena_1.47.0.tgz |
| macOS Binary (sonoma-arm64) | cogena_1.47.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cogena |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cogena |
| Bioc Package Browser | https://code.bioconductor.org/browse/cogena/ |
| Package Short Url | https://bioconductor.org/packages/cogena/ |
| Package Downloads Report | Download Stats |