To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SMITE")
In most cases, you don't need to download the package archive at all.
SMITE
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see SMITE.
Significance-based Modules Integrating the Transcriptome and Epigenome
Bioconductor version: 3.3
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SMITE")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SMITE")
| R Script | SMITE Tutorial | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Coverage, DifferentialExpression, DifferentialMethylation, GenomeAnnotation, Network, NetworkEnrichment, RNASeq, Sequencing, Software, SystemsBiology |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.3 (R-3.3) (< 6 months) |
| 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 |
| LinkingTo | |
| Suggests | knitr |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/GreallyLab/SMITE |
| BugReports | https://github.com/GreallyLab/SMITE/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | SMITE_1.0.2.tar.gz |
| Windows Binary | SMITE_1.0.2.zip |
| Mac OS X 10.9 (Mavericks) | SMITE_1.0.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/SMITE/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/SMITE/ |
| Package Downloads Report | Download Stats |
Documentation »
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