Man pages for almeidasilvaf/BioNERO
Biological Network Reconstruction Omnibus
| BioNERO-package | BioNERO: Biological Network Reconstruction Omnibus |
| 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... |
| 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... |
| enrichment_analysis | Perform overrepresentation analysis for a set of genes |
| 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... |
| exp2grn | Infer gene regulatory network from expression data |
| exp_genes2orthogroups | Collapse gene-level expression data to orthogroup level |
| exp_preprocess | Preprocess expression data for network reconstruction |
| filter_by_variance | Keep only genes with the highest variances |
| filt.se | Filtered maize gene expression data from Shin et al., 2021. |
| 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... |
| grn_combined | Infer gene regulatory network with multiple algorithms and... |
| grn_filter | Filter a gene regulatory network based on optimal scale-free... |
| grn_infer | Infer gene regulatory network with one of three algorithms |
| is_singleton | Logical expression to check if gene or gene set is singleton... |
| modPres_netrep | Calculate module preservation between two expression data... |
| modPres_WGCNA | Calculate module preservation between two expression data... |
| module_enrichment | Perform enrichment analysis for coexpression network modules |
| module_preservation | Calculate network preservation between two expression data... |
| 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... |
| 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... |
| 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... |
| 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... |
| zma.interpro | Maize Interpro annotation |
| zma.se | Maize gene expression data from Shin et al., 2021. |
| zma.tfs | Maize transcription factors |
