.get_correlates | .get_correlates |
.plot_one_interaction | Network visualization |
discretize | Set the discretized expression attribute Uses the discretize_exprs function of the FCBF package |
discretize-method | Set the discretized expression attribute Uses the discretize_exprs function of the FCBF package |
fc | Example fcoex object |
fcoex-class | An S4 class to represent the fcoex analysis. |
find_cbf_modules | find_cbf_modules |
find_cbf_modules-method | find_cbf_modules |
get_nets | Network visualization |
get_nets-method | Network visualization |
idents | Retrieves module identities from the recluster function |
idents-method | Retrieves module identities from the recluster function |
mini_pbmc3k | Processed subset of the pbmc3k dataset from PBMC genomics |
module_genes | Get the module genes in a fcoex object |
module_genes-method | Get the module genes in a fcoex object |
mod_colors | Set module colors mod_colors attribute |
mod_colors-method | Set module colors mod_colors attribute |
mod_gene_num | Get the number of genes in modules in a fcoex object This function was copied and adapted from the CEMiTool package. |
mod_gene_num-method | Get the number of genes in modules in a fcoex object This function was copied and adapted from the CEMiTool package. |
mod_names | Get module names in a fcoex object |
mod_names-method | Get module names in a fcoex object |
mod_ora | Over Representation Analysis (ORA) |
mod_ora-method | Over Representation Analysis (ORA) |
new_fcoex | Create a fcoex object |
nmodules | Get the number of modules in a fcoex object |
nmodules-method | Get the number of modules in a fcoex object |
ora_data | Retrieve over representation analysis (ORA) results |
ora_data-method | Retrieve over representation analysis (ORA) results |
plot_ora | ORA visualization |
plot_ora-method | ORA visualization |
recluster | Recluster cells based on fcoex module composition |
recluster-method | Recluster cells based on fcoex module composition |
save_plots | Save fcoex object plots |
save_plots-method | Save fcoex object plots |
show-method | Print a fcoex object |
show_net | Retrieve fcoex net plots |
show_net-method | Retrieve fcoex net plots |
show_ora | Retrieve fcoex ora plots |
show_ora-method | Retrieve fcoex ora plots |