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