adSplit
This is the development version of adSplit; for the stable release version, see adSplit.
Annotation-Driven Clustering
Bioconductor version: Development (3.24)
This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.
Author: Claudio Lottaz, Joern Toedling
Maintainer: Claudio Lottaz <Claudio.Lottaz at klinik.uni-regensburg.de>
citation("adSplit")):
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("adSplit")
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("adSplit")| Annotation-Driven Clustering | R Script | |
| Reference Manual |
Details
| biocViews | Clustering, Microarray, Software |
| Version | 1.83.0 |
| In Bioconductor since | BioC 1.8 (R-2.3) (20.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.1.0), methods (>= 2.1.0) |
| Imports | AnnotationDbi, Biobase(>= 1.5.12), cluster (>= 1.9.1), GO.db(>= 1.8.1), graphics, grDevices, KEGGREST(>= 1.30.1), multtest(>= 1.6.0), stats (>= 2.1.0) |
| System Requirements | |
| URL | http://compdiag.molgen.mpg.de/software/adSplit.shtml |
See More
| Suggests | golubEsets(>= 1.0), vsn(>= 1.5.0), hu6800.db(>= 1.8.1) |
| 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 | adSplit_1.83.0.tar.gz |
| Windows Binary (x86_64) | adSplit_1.83.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | adSplit_1.83.0.tgz |
| macOS Binary (sonoma-arm64) | adSplit_1.83.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/adSplit |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/adSplit |
| Bioc Package Browser | https://code.bioconductor.org/browse/adSplit/ |
| Package Short Url | https://bioconductor.org/packages/adSplit/ |
| Package Downloads Report | Download Stats |