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SMITE

Significance-based Modules Integrating the Transcriptome and Epigenome


Bioconductor version: Release (3.18)

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 <nawijet at gmail.com>, Andrew Damon Johnston <Andrew.Johnston at med.einstein.yu.edu>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SMITE")

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("SMITE")
SMITE Tutorial PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, DifferentialExpression, DifferentialMethylation, GenomeAnnotation, ImmunoOncology, Network, NetworkEnrichment, RNASeq, Sequencing, Software, SystemsBiology
Version 1.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL (>=2)
Depends R (>= 3.5), GenomicRanges
Imports scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2, reactome.db, KEGGREST, BioNet, goseq, methods, IRanges, igraph, Biobase, tools, S4Vectors, geneLenDataBase, grDevices, graphics, stats, utils
System Requirements
URL https://github.com/GreallyLab/SMITE
Bug Reports https://github.com/GreallyLab/SMITE/issues
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Package Archives

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

Source Package SMITE_1.30.0.tar.gz
Windows Binary SMITE_1.30.0.zip
macOS Binary (x86_64) SMITE_1.30.0.tgz
macOS Binary (arm64) SMITE_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SMITE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SMITE
Bioc Package Browser https://code.bioconductor.org/browse/SMITE/
Package Short Url https://bioconductor.org/packages/SMITE/
Package Downloads Report Download Stats