SMITE

This is the development version of SMITE; for the stable release version, see SMITE.

Significance-based Modules Integrating the Transcriptome and Epigenome

Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SMITE")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DifferentialExpression, DifferentialMethylation, GenomeAnnotation, ImmunoOncology, Network, NetworkEnrichment, RNASeq, Sequencing, Software, SystemsBiology
Version	1.31.0
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

Suggests	knitr, rmarkdown
Linking To
Enhances
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/SMITE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SMITE
Package Short Url	https://bioconductor.org/packages/SMITE/
Package Downloads Report	Download Stats