adj_data	adj_data
adj_data,CEMiTool-method	adj_data
adj_data<-	adj_data
adj_data<-,CEMiTool-method	adj_data
cem	cem
cemitool	cemitool
CEMiTool-class	CEMiTool-class
diagnostic_report	diagnostic_report
diagnostic_report,CEMiTool-method	diagnostic_report
expr0	expr0
expr_data	expr_data
expr_data,CEMiTool-method	expr_data
expr_data<-	expr_data
expr_data<-,CEMiTool-method	expr_data
expr_pct_filter	expr_pct_filter
filter_genes	filter_expr
find_modules	find_modules
find_modules,CEMiTool-method	find_modules
fit_data	fit_data
fit_data,CEMiTool-method	fit_data
generate_report	generate_report
generate_report,CEMiTool-method	generate_report
get_adj	get_adj
get_adj,CEMiTool-method	get_adj
get_beta_data	get_beta_data
get_beta_data,CEMiTool-method	get_beta_data
get_cemitool_r2_beta	get_cemitool_r2_beta
get_cemitool_r2_beta,CEMiTool-method	get_cemitool_r2_beta
get_connectivity	get_connectivity
get_connectivity,CEMiTool-method	get_connectivity
get_hubs	get_hubs
get_hubs,CEMiTool-method	get_hubs
get_merged_mods	get_merged_mods
get_merged_mods,CEMiTool-method	get_merged_mods
get_mods	get_mods
get_mods,CEMiTool-method	get_mods
get_phi	get_phi
get_phi,CEMiTool-method	get_phi
gsea_data	gsea_data
gsea_data,CEMiTool-method	gsea_data
interactions_data	interactions_data
interactions_data,CEMiTool-method	interactions_data
interactions_data<-	interactions_data
interactions_data<-,CEMiTool-method	interactions_data
module_genes	module_genes
module_genes,CEMiTool-method	module_genes
module_to_gmt	module_to_gmt
mod_colors	mod_colors
mod_colors,CEMiTool-method	mod_colors
mod_colors<-	mod_colors
mod_colors<-,CEMiTool,character-method	mod_colors
mod_gene_num	mod_gene_num
mod_gene_num,CEMiTool-method	mod_gene_num
mod_gsea	mod_gsea
mod_gsea,CEMiTool-method	mod_gsea
mod_names	mod_names
mod_names,CEMiTool-method	mod_names
mod_ora	mod_ora
mod_ora,CEMiTool-method	mod_ora
mod_summary	mod_summary
mod_summary,CEMiTool-method	mod_summary
new_cem	new_cem
nmodules	nmodules
nmodules,CEMiTool-method	nmodules
ora_data	ora_data
ora_data,CEMiTool-method	ora_data
plot_beta_r2	plot_beta_r2
plot_beta_r2,CEMiTool-method	plot_beta_r2
plot_gsea	plot_gsea
plot_gsea,CEMiTool-method	plot_gsea
plot_hist	plot_hist
plot_hist,CEMiTool-method	plot_hist
plot_interactions	plot_interactions
plot_interactions,CEMiTool-method	plot_interactions
plot_mean_k	plot_mean_k
plot_mean_k,CEMiTool-method	plot_mean_k
plot_mean_var	plot_mean_var
plot_mean_var,CEMiTool-method	plot_mean_var
plot_ora	plot_ora
plot_ora,CEMiTool-method	plot_ora
plot_ora_single	plot_ora_single
plot_profile	plot_profile
plot_profile,CEMiTool-method	plot_profile
plot_qq	plot_qq
plot_qq,CEMiTool-method	plot_qq
plot_sample_tree	plot_sample_tree
plot_sample_tree,CEMiTool-method	plot_sample_tree
read_gmt	read_gmt
sample_annot	sample_annot
sample_annotation	sample_annotation
sample_annotation,CEMiTool-method	sample_annotation
sample_annotation<-	sample_annotation
sample_annotation<-,CEMiTool-method	sample_annotation
save_plots	save_plots
save_plots,CEMiTool-method	save_plots
select_genes	select_genes
show,CEMiTool-method	show-CEMiTool-method
show_plot	show_plot
show_plot,CEMiTool-method	show_plot
vst	vst
write_files	write_files
write_files,CEMiTool-method	write_files
