SMITE

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see SMITE.

Significance-based Modules Integrating the Transcriptome and Epigenome

Bioconductor version: 3.9

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 (version "3.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DifferentialExpression, DifferentialMethylation, GenomeAnnotation, ImmunoOncology, Network, NetworkEnrichment, RNASeq, Sequencing, Software, SystemsBiology
Version	1.12.0
In Bioconductor since	BioC 3.3 (R-3.3) (8 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
System Requirements
URL	https://github.com/GreallyLab/SMITE
Bug Reports	https://github.com/GreallyLab/SMITE/issues

Suggests	knitr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	SMITE_1.12.0.tar.gz
Windows Binary	SMITE_1.12.0.zip
Mac OS X 10.11 (El Capitan)	SMITE_1.12.0.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
Old Source Packages for BioC 3.9	Source Archive