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Bioconductor - SMITE

SMITE

This is the released version of SMITE; for the devel version, see SMITE.

Significance-based Modules Integrating the Transcriptome and Epigenome

Bioconductor version: Release (3.21)

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 "4.5") 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")
Details biocViews Coverage, DifferentialExpression, DifferentialMethylation, GenomeAnnotation, ImmunoOncology, Network, NetworkEnrichment, RNASeq, Sequencing, Software, SystemsBiology Version 1.36.0 In Bioconductor since BioC 3.3 (R-3.3) (9 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 See More Package Archives

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

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