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

## Documentation for package ‘SGCP’ version 1.10.0

- DESCRIPTION file.
- 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