To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("SANTA")
In most cases, you don't need to download the package archive at all.
SANTA
Spatial Analysis of Network Associations
Bioconductor version: 3.0
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 J. Cornish and Florian Markowetz
Maintainer: Alex J. Cornish <a.cornish12 at imperial.ac.uk>
Citation (from within R,
enter citation("SANTA")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("SANTA")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SANTA")
| HTML | R Script | Introduction to SANTA |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Clustering, Network, NetworkEnrichment, Software |
| Version | 2.2.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) |
| License | GPL (>= 2) |
| Depends | R (>= 2.14), igraph |
| Imports | Matrix, snow, stringr |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics, knitr, knitcitations, formatR, org.Sc.sgd.db, BioNet, DLBCL, msm |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | SANTA_2.2.0.tar.gz |
| Windows Binary | SANTA_2.2.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | SANTA_2.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | SANTA_2.2.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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