EGSEA123
This is the development version of EGSEA123; for the stable release version, see EGSEA123.
Easy and efficient ensemble gene set testing with EGSEA
Bioconductor version: Development (3.24)
R package that supports the workflow article `Easy and efficient ensemble gene set testing with EGSEA', Alhamdoosh et al. (2017), F1000Research, 6:2010.
Author: Monther Alhamdoosh, Charity Law, Luyi Tian, Julie Sheridan, Milica Ng and Matthew Ritchie
Maintainer: Matthew Ritchie <mritchie at wehi.edu.au>
citation("EGSEA123")):
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("EGSEA123")
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("EGSEA123")| Easy and efficient ensemble gene set testing with EGSEA | HTML | R Script |
Details
| biocViews | GeneExpressionWorkflow, ImmunoOncologyWorkflow, Workflow |
| Version | 1.37.0 |
| License | Artistic-2.0 |
| Depends | R (>= 3.4.0), EGSEA(>= 1.5.2), limma(>= 3.49.2), edgeR, illuminaio |
| Imports | |
| System Requirements | |
| URL | https://f1000research.com/articles/6-2010 |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EGSEA123_1.37.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/EGSEA123 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/EGSEA123 |
| Package Short Url | https://bioconductor.org/packages/EGSEA123/ |
| Package Downloads Report | Download Stats |