Package: SMITE
Type: Package
Title: Significance-based Modules Integrating the Transcriptome and
        Epigenome
Version: 1.2.0
Date: 2016-01-01
Author: Neil Ari Wijetunga, Andrew Damon Johnston, John Murray Greally
Maintainer: Neil Ari Wijetunga <Neil.Wijetunga@med.einstein.yu.edu>,
 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 (>= 3.3), 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
Suggests: knitr
VignetteBuilder: knitr
biocViews: DifferentialMethylation, DifferentialExpression,
        SystemsBiology, NetworkEnrichment,GenomeAnnotation,Network,
        Sequencing, RNASeq, Coverage
URL: https://github.com/GreallyLab/SMITE
BugReports: https://github.com/GreallyLab/SMITE/issues
NeedsCompilation: no
Packaged: 2016-10-18 00:29:11 UTC; biocbuild
Built: R 3.3.1; ; 2016-10-18 04:50:43 UTC; windows
