SMITE

DOI: 10.18129/B9.bioc.SMITE  

Significance-based Modules Integrating the Transcriptome and Epigenome

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	SMITE Tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, DifferentialExpression, DifferentialMethylation, GenomeAnnotation, ImmunoOncology, Network, NetworkEnrichment, RNASeq, Sequencing, Software, SystemsBiology
Version	1.26.0
In Bioconductor since	BioC 3.3 (R-3.3) (7 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
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/GreallyLab/SMITE
BugReports	https://github.com/GreallyLab/SMITE/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	SMITE_1.26.0.tar.gz
Windows Binary	SMITE_1.26.0.zip (64-bit only)
macOS Binary (x86_64)	SMITE_1.26.0.tgz
macOS Binary (arm64)	SMITE_1.26.0.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