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SGCP

This is the development version of SGCP; for the stable release version, see SGCP.

SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expression networks


Bioconductor version: Development (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 (from within R, enter citation("SGCP")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews Classification, Clustering, DimensionReduction, GeneExpression, GeneSetEnrichment, GraphAndNetwork, Network, NetworkEnrichment, NeuralNetwork, RNASeq, Software, SystemsBiology, Visualization, mRNAMicroarray
Version 1.3.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends R (>= 4.3.0)
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
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Suggests knitr, BiocManager
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SGCP_1.3.0.tar.gz
Windows Binary SGCP_1.3.0.zip
macOS Binary (x86_64) SGCP_1.3.0.tgz
macOS Binary (arm64) SGCP_1.3.0.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