SGCP
This is thereleased version of SGCP; for the devel version, seeSGCP.
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expression networks
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0003-1096-7592, Ioannis Koutis [aut]
Maintainer: Niloofar AghaieAbiane <niloofar.abiane at gmail.com>
citation("SGCP")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("SGCP")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Classification,Clustering,DimensionReduction,GeneExpression,GeneSetEnrichment,GraphAndNetwork,Network,NetworkEnrichment,NeuralNetwork,RNASeq,Software,SystemsBiology,Visualization,mRNAMicroarray |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (2.5 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 | |
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| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | SGCP_1.9.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |