CEMiTool-class          An S4 class to represent the CEMiTool analysis.
adj_data                Get or set adjacency matrix value
cem                     CEMiTool Object
cemitool                Full gene co-expression analysis
diagnostic_report       Diagnostic report
expr0                   Yellow Fever gene expression data from GEO
                        study GSE13485
expr_data               Retrieve and set expression attribute
filter_genes            Filter a gene expression data.frame
find_modules            Co-expression modules definition
fit_data                Retrieve scale-free model fit data
generate_report         CEMiTool report
get_adj                 Calculate adjacency matrix
get_beta_data           Soft-threshold beta data
get_cemitool_r2_beta    Calculate CEMiTool beta and R2 values
get_connectivity        Calculate network connectivity
get_hubs                Get hubs
get_merged_mods         Merge similar modules
get_mods                Calculate co-expression modules
get_phi                 Calculate phi
gsea_data               Retrieve Gene Set Enrichment Analysis (GSEA)
                        results
interactions_data       Retrieve and set interaction data to CEMiTool
                        object
mod_colors              Retrieve and set mod_colors attribute
mod_gene_num            Get the number of genes in modules in a
                        CEMiTool object
mod_gsea                Module Gene Set Enrichment Analysis
mod_names               Get module names in a CEMiTool object
mod_ora                 Module Overrepresentation Analysis
mod_summary             Co-expression module summarization
module_genes            Get the module genes in a CEMiTool object
new_cem                 Create a CEMiTool object
nmodules                Get the number of modules in a CEMiTool object
ora_data                Retrieve over representation analysis (ORA)
                        results
plot_beta_r2            Soft-threshold beta selection graph
plot_gsea               GSEA visualization
plot_hist               Plot histogram
plot_interactions       Network visualization
plot_mean_k             Network mean connectivity
plot_mean_var           Plot mean and variance
plot_ora                ORA visualization
plot_profile            Expression profile visualization
plot_qq                 Plot quantile-quantile plot
plot_sample_tree        Sample clustering
read_gmt                Read a GMT file
sample_annot            Yellow Fever Sample Annotation data
sample_annotation       Retrive or set the sample_annotation attribute
save_plots              Save CEMiTool object plots
select_genes            Select genes based on variance
show,CEMiTool-method    Print a cemitool object
show_plot               Retrieve CEMiTool object plots
write_files             Save the CEMiTool object in files
