SPIA
This is the released version of SPIA; for the devel version, see SPIA.
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
Bioconductor version: Release (3.23)
This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.
Author: Adi Laurentiu Tarca <atarca at med.wayne.edu>, Purvesh Kathri <purvesh at cs.wayne.edu> and Sorin Draghici <sorin at wayne.edu>
Maintainer: Adi Laurentiu Tarca <atarca at med.wayne.edu>
citation("SPIA")):
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("SPIA")
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("SPIA")| SPIA | R Script | |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | GraphAndNetwork, Microarray, Software |
| Version | 2.64.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (17.5 years) |
| License | file LICENSE |
| Depends | R (>= 2.14.0), graphics, KEGGgraph |
| Imports | graphics |
| System Requirements | |
| URL | http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1 |
See More
| Suggests | graph, Rgraphviz, hgu133plus2.db |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | EnrichmentBrowser |
| Suggests Me | graphite, KEGGgraph |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SPIA_2.64.0.tar.gz |
| Windows Binary (x86_64) | SPIA_2.64.0.zip |
| macOS Binary (big-sur-x86_64) | SPIA_2.64.0.tgz |
| macOS Binary (sonoma-arm64) | SPIA_2.64.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SPIA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SPIA |
| Bioc Package Browser | https://code.bioconductor.org/browse/SPIA/ |
| Package Short Url | https://bioconductor.org/packages/SPIA/ |
| Package Downloads Report | Download Stats |