Biological Network Reconstruction Omnibus

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Documentation for package ‘BioNERO’ version 1.0.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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
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 enrichment analysis for a set of genes
exp2gcn	Reconstruct gene coexpression network from gene expression
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
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_hubs_ppi	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_dendro_and_cons_colors	Plot dendrogram of genes and consensus 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_grn	Plot gene regulatory network from edge list
plot_heatmap	Plot heatmap of hierarchically clustered sample correlations or gene expression
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