SMITE

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Significance-based Modules Integrating the Transcriptome and Epigenome

Bioconductor version: Development (3.24)

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")):

Neil Ari Wijetunga, Andrew Damon Johnston, John Murray Greally. SMITE: Significance-based Modules Integrating the Transcriptome and Epigenome. doi:10.18129/B9.bioc.SMITE, R package version 1.41.0, https://bioconductor.org/packages/SMITE.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DifferentialExpression, DifferentialMethylation, GenomeAnnotation, ImmunoOncology, Network, NetworkEnrichment, RNASeq, Sequencing, Software, SystemsBiology
Version	1.41.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 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
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	SMITE_1.41.0.tar.gz
Windows Binary (x86_64)	SMITE_1.41.0.zip
macOS Binary (big-sur-x86_64)	SMITE_1.41.0.tgz
macOS Binary (sonoma-arm64)	SMITE_1.41.0.tgz
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