To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SMITE")

In most cases, you don't need to download the package archive at all.

SMITE

DOI: 10.18129/B9.bioc.SMITE    

Significance-based Modules Integrating the Transcriptome and Epigenome

Bioconductor version: Release (3.6)

This package builds on the Epimods framework which facilitates finding weighted subnetworks ("modules") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules.

Author: Neil Ari Wijetunga, Andrew Damon Johnston, John Murray Greally

Maintainer: Neil Ari Wijetunga <Neil.Wijetunga at med.einstein.yu.edu>, Andrew Damon Johnston <Andrew.Johnston at med.einstein.yu.edu>

Citation (from within R, enter citation("SMITE")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SMITE")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SMITE")

 

PDF R Script SMITE Tutorial
PDF   Reference Manual
Text   NEWS

Details

biocViews Coverage, DifferentialExpression, DifferentialMethylation, GenomeAnnotation, Network, NetworkEnrichment, RNASeq, Sequencing, Software, SystemsBiology
Version 1.6.0
In Bioconductor since BioC 3.3 (R-3.3) (1.5 years)
License GPL (>=2)
Depends R (>= 3.3), GenomicRanges
Imports scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2, reactome.db, KEGG.db, BioNet, goseq, methods, IRanges, igraph, Biobase, tools, S4Vectors, geneLenDataBase, grDevices, graphics, stats, utils
LinkingTo
Suggests knitr
SystemRequirements
Enhances
URL https://github.com/GreallyLab/SMITE
BugReports https://github.com/GreallyLab/SMITE/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SMITE_1.6.0.tar.gz
Windows Binary SMITE_1.6.0.zip
Mac OS X 10.11 (El Capitan) SMITE_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SMITE
Package Short Url http://bioconductor.org/packages/SMITE/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: