SGCP
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see SGCP.
SGCP: a spectral self-learning method for clustering genes in co-expression networks
Bioconductor version: 3.19
SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks. SGC consists of multiple novel steps that enable the computation of highly enriched modules in an unsupervised manner. But unlike all existing frameworks, it further incorporates a novel step that leverages Gene Ontology information in a semi-supervised clustering method that further improves the quality of the computed modules.
Author: Niloofar AghaieAbiane [aut, cre] 
, Ioannis Koutis [aut]
Maintainer: Niloofar AghaieAbiane <niloofar.abiane at gmail.com>
citation("SGCP")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SGCP")
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("SGCP")| SGCP package manual | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, DimensionReduction, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Network, NetworkEnrichment, NeuralNetwork, RNASeq, Software, SystemsBiology, Visualization, mRNAMicroarray |
| Version | 1.4.4 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.2.0) |
| Imports | ggplot2, expm, caret, plyr, dplyr, GO.db, annotate, SummarizedExperiment, genefilter, GOstats, RColorBrewer, xtable, Rgraphviz, reshape2, openxlsx, ggridges, DescTools, org.Hs.eg.db, methods, grDevices, stats, RSpectra, graph |
| System Requirements | |
| URL | https://github.com/na396/SGCP |
See More
| Suggests | knitr, rmarkdown, BiocManager, devtools, BiocStyle |
| 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 | SGCP_1.4.4.tar.gz |
| Windows Binary (x86_64) | SGCP_1.4.4.zip |
| macOS Binary (x86_64) | SGCP_1.4.4.tgz |
| macOS Binary (arm64) | SGCP_1.4.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SGCP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SGCP |
| Bioc Package Browser | https://code.bioconductor.org/browse/SGCP/ |
| Package Short Url | https://bioconductor.org/packages/SGCP/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |