SMITE
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see SMITE.
Significance-based Modules Integrating the Transcriptome and Epigenome
Bioconductor version: 3.17
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("SMITE")):
Installation
To install this package, start R (version "4.3") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, DifferentialExpression, DifferentialMethylation, GenomeAnnotation, ImmunoOncology, Network, NetworkEnrichment, RNASeq, Sequencing, Software, SystemsBiology |
| Version | 1.28.0 |
| 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 |
See More
| 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_1.28.0.tar.gz |
| Windows Binary | SMITE_1.28.0.zip |
| macOS Binary (x86_64) | SMITE_1.28.0.tgz |
| macOS Binary (arm64) | SMITE_1.28.0.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 3.17 | Source Archive |