DExMA
This is the released version of DExMA; for the devel version, see DExMA.
Differential Expression Meta-Analysis
Bioconductor version: Release (3.23)
performing all the steps of gene expression meta-analysis considering the possible existence of missing genes. It provides the necessary functions to be able to perform the different methods of gene expression meta-analysis. In addition, it contains functions to apply quality controls, download GEO datasets and show graphical representations of the results.
Author: Juan Antonio Villatoro-García [aut, cre], Pedro Carmona-Sáez [aut]
Maintainer: Juan Antonio Villatoro-García <juanantoniovillatorogarcia at gmail.com>
citation("DExMA")):
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")
BiocManager::install("DExMA")
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("DExMA")| Differential Expression Meta-Analysis with DExMA package | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, QualityControl, Software, StatisticalMethod |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | GPL-2 |
| Depends | R (>= 4.1), DExMAdata |
| Imports | Biobase, GEOquery, impute, limma, pheatmap, plyr, scales, snpStats, sva, swamp, stats, methods, utils, bnstruct, RColorBrewer, grDevices |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, qpdf, BiocGenerics, RUnit |
| 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 | DExMA_1.20.0.tar.gz |
| Windows Binary (x86_64) | DExMA_1.20.0.zip |
| macOS Binary (big-sur-x86_64) | DExMA_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | DExMA_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DExMA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DExMA |
| Bioc Package Browser | https://code.bioconductor.org/browse/DExMA/ |
| Package Short Url | https://bioconductor.org/packages/DExMA/ |
| Package Downloads Report | Download Stats |