FCBF-based Co-Expression Networks for Single Cells


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Documentation for package ‘fcoex’ version 1.13.0

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.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