Package: SMITE
Type: Package
Title: Significance-based Modules Integrating the Transcriptome and
        Epigenome
Version: 1.39.0
Date: 2021-11-21
Author: Neil Ari Wijetunga, Andrew Damon Johnston, John Murray Greally
Maintainer: Neil Ari Wijetunga <nawijet@gmail.com>, Andrew Damon
 Johnston <Andrew.Johnston@med.einstein.yu.edu>
Description: 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.
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
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
biocViews: ImmunoOncology, DifferentialMethylation,
        DifferentialExpression, SystemsBiology,
        NetworkEnrichment,GenomeAnnotation,Network, Sequencing, RNASeq,
        Coverage
URL: https://github.com/GreallyLab/SMITE
BugReports: https://github.com/GreallyLab/SMITE/issues
NeedsCompilation: no
Config/pak/sysreqs: libglpk-dev make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:29:51 UTC
RemoteUrl: https://github.com/bioc/SMITE
RemoteRef: HEAD
RemoteSha: cf2f9aecebbf6e1aa0ea6f15fd290550b9d69d32
Packaged: 2026-02-17 08:47:48 UTC; root
Built: R 4.6.0; ; 2026-02-17 08:50:59 UTC; unix
