check_SFT               Check scale-free topology fit for a given
                        network
consensus_modules       Identify consensus modules across independent
                        data sets
consensus_SFT_fit       Pick power to fit networks to scale-free
                        topology
consensus_trait_cor     Correlate set-specific modules and consensus
                        modules to sample information
cor2adj                 Calculate an adjacency matrix from a
                        correlation matrix
cormat_to_edgelist      Transform a correlation matrix to an edge list
detect_communities      Detect communities in a network
dfs2one                 Combine multiple expression tables (.tsv) into
                        a single data frame
enrichment_analysis     Perform overrepresentation analysis for a set
                        of genes
exp_genes2orthogroups   Collapse gene-level expression data to
                        orthogroup level
exp_preprocess          Preprocess expression data for network
                        reconstruction
exp2cor                 Calculate pairwise correlations between genes
                        in a matrix
exp2gcn                 Infer gene coexpression network from gene
                        expression
exp2gcn_blockwise       Infer gene coexpression network from gene
                        expression in a blockwise manner
exp2grn                 Infer gene regulatory network from expression
                        data
filt.se                 Filtered maize gene expression data from Shin
                        et al., 2021.
filter_by_variance      Keep only genes with the highest variances
gene_significance       Calculate gene significance for a given group
                        of genes
get_edge_list           Get edge list from an adjacency matrix for a
                        group of genes
get_HK                  Get housekeeping genes from global expression
                        profile
get_hubs_gcn            Get GCN hubs
get_hubs_grn            Get hubs for gene regulatory network
get_neighbors           Get 1st-order neighbors of a given gene or
                        group of genes
grn_average_rank        Rank edge weights for GRNs and calculate
                        average across different methods
grn_combined            Infer gene regulatory network with multiple
                        algorithms and combine results in a list
grn_filter              Filter a gene regulatory network based on
                        optimal scale-free topology fit
grn_infer               Infer gene regulatory network with one of three
                        algorithms
is_singleton            Logical expression to check if gene or gene set
                        is singleton or not
modPres_netrep          Calculate module preservation between two
                        expression data sets using NetRep's algorithm
modPres_WGCNA           Calculate module preservation between two
                        expression data sets using WGCNA's algorithm
module_enrichment       Perform enrichment analysis for coexpression
                        network modules
module_preservation     Calculate network preservation between two
                        expression data sets
module_stability        Perform module stability analysis
module_trait_cor        Correlate module eigengenes to trait
net_stats               Calculate network statistics
og.zma.osa              Orthogroups between maize and rice
osa.se                  Rice gene expression data from Shin et al.,
                        2021.
parse_orthofinder       Parse orthogroups identified by OrthoFinder
PC_correction           Apply Principal Component (PC)-based correction
                        for confounding artifacts
plot_dendro_and_colors
                        Plot dendrogram of genes and modules
plot_eigengene_network
                        Plot eigengene network
plot_expression_profile
                        Plot expression profile of given genes across
                        samples
plot_gcn                Plot gene coexpression network from edge list
plot_gene_significance
                        Plot a heatmap of gene significance
plot_grn                Plot gene regulatory network from edge list
plot_heatmap            Plot heatmap of hierarchically clustered sample
                        correlations or gene expression
plot_module_trait_cor   Plot a heatmap of module-trait correlations
plot_ngenes_per_module
                        Plot number of genes per module
plot_PCA                Plot Principal Component Analysis (PCA) of
                        samples
plot_ppi                Plot protein-protein interaction network from
                        edge list
q_normalize             Quantile normalize the expression data
remove_nonexp           Remove genes that are not expressed based on a
                        user-defined threshold
replace_na              Remove missing values in a gene expression data
                        frame
SFT_fit                 Pick power to fit network to a scale-free
                        topology
ZKfiltering             Filter outlying samples based on the
                        standardized connectivity (Zk) method
zma.interpro            Maize Interpro annotation
zma.se                  Maize gene expression data from Shin et al.,
                        2021.
zma.tfs                 Maize transcription factors
