SANTA
This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see SANTA.
Spatial Analysis of Network Associations
Bioconductor version: Release (3.23)
This package provides methods for measuring the strength of association between a network and a phenotype. It does this by measuring clustering of the phenotype across the network (Knet). Vertices can also be individually ranked by their strength of association with high-weight vertices (Knode).
Author: Alex Cornish [cre, aut]
Maintainer: Alex Cornish <alexcornish88 at gmail.com>
citation("SANTA")):
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("SANTA")
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("SANTA")| Introduction to SANTA | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, Network, NetworkEnrichment, Software |
| Version | 2.48.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 4.1), igraph |
| Imports | graphics, Matrix, methods, stats |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/alexjcornish/SANTA |
See More
| Suggests | BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db, markdown, rmarkdown, 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 | SANTA_2.48.0.tar.gz |
| Windows Binary (x86_64) | SANTA_2.48.0.zip |
| macOS Binary (big-sur-x86_64) | SANTA_2.48.0.tgz |
| macOS Binary (sonoma-arm64) | SANTA_2.48.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SANTA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SANTA |
| Bioc Package Browser | https://code.bioconductor.org/browse/SANTA/ |
| Package Short Url | https://bioconductor.org/packages/SANTA/ |
| Package Downloads Report | Download Stats |