SMITE

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SMITE.

Significance-based Modules Integrating the Transcriptome and Epigenome

Bioconductor version: 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>

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

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")

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 1.26.0

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

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_1.26.0.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

Old Source Packages for BioC 3.16 Source Archive