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

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Documentation for package ‘SGCP’ version 1.9.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

adjacencyMatrix	Performs netwrok construction step in the SGCP pipeline
cheng	Normalized gene expression data from Cheng et al.'s publication on ischemic cardiomyopathy (ICM).
clustering	Perform network clustering step in the SGCP pipeline
ezSGCP	Integrated execution of the SGCP pipeline
geneOntology	Performs gene ontology enrichment step in the SGCP pipeline.
resClus	An example of the output from 'clustering' function in the SGCP pipeline
resFinalGO	An example of the output from 'geneOntololgy' function in the SGCP pipeline
resInitialGO	An example of the output from the 'geneOntololgy' function in the SGCP pipeline
resSemiLabel	An example of the output from 'semiLabeling' function in the SGCP pipeline
resSemiSupervised	An example of the output from 'semiSupervised' function in the SGCP pipeline
semiLabeling	Performs gene semi-labeling step in the SGCP pipeline
semiSupervised	Performs the semi-supervised step in the SGCP pipeline
sgcp	An example of the output of 'ezSGCP' function in the SGCP pipeline
SGCP_ezPLOT	Comprehensive SGCP plotting in one execution
SGCP_plot_bar	Mean p-value bar chart for gene ontology enrichment in the SGCP pipeline
SGCP_plot_conductance	Cluster conductance index bar chart in the SGCP Pipeline
SGCP_plot_density	Visualization of gene ontology term p-value distribution in the SGCP pipeline
SGCP_plot_heatMap	Adjacency matrix heatmap in the SGCP pipeline
SGCP_plot_jitter	P-value jitter chart for gene ontology enrichment in the SGCP pipeline.
SGCP_plot_pca	PCA visualization in the SGCP Pipeline
SGCP_plot_pie	Gene ontology analysis pie chart in the SGCP pipeline
SGCP_plot_silhouette	Cluster silhouette index chart in the SGCP Pipeline