GeneExpressionSignature
This is the development version of GeneExpressionSignature; for the stable release version, see GeneExpressionSignature.
Gene Expression Signature based Similarity Metric
Bioconductor version: Development (3.24)
This package gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.
Author: Yang Cao [aut, cre], Fei Li [ctb], Lu Han [ctb]
Maintainer: Yang Cao <yiluheihei at gmail.com>
citation("GeneExpressionSignature")):
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("GeneExpressionSignature")
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("GeneExpressionSignature")| GeneExpressionSignature | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Software |
| Version | 1.59.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (15 years) |
| License | GPL-2 |
| Depends | R (>= 4.0) |
| Imports | Biobase, stats, methods |
| System Requirements | |
| URL | https://github.com/yiluheihei/GeneExpressionSignature |
| Bug Reports | https://github.com/yiluheihei/GeneExpressionSignature/issues/ |
See More
| Suggests | apcluster, GEOquery, knitr, rmarkdown, BiocStyle |
| 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 | GeneExpressionSignature_1.59.0.tar.gz |
| Windows Binary (x86_64) | GeneExpressionSignature_1.59.0.zip |
| macOS Binary (big-sur-x86_64) | GeneExpressionSignature_1.59.0.tgz |
| macOS Binary (sonoma-arm64) | GeneExpressionSignature_1.59.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GeneExpressionSignature |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GeneExpressionSignature |
| Bioc Package Browser | https://code.bioconductor.org/browse/GeneExpressionSignature/ |
| Package Short Url | https://bioconductor.org/packages/GeneExpressionSignature/ |
| Package Downloads Report | Download Stats |