├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ └── check-bioc.yml ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── BioNERO-package.R ├── consensus_modules.R ├── data.R ├── data_preprocess.R ├── evolutionary_analysis.R ├── exploratory_analysis.R ├── gcn_inference.R ├── grn_inference.R ├── network_comparison.R ├── network_stats.R ├── network_visualization.R └── utils.R ├── README.Rmd ├── README.md ├── codecov.yml ├── data ├── filt.se.rda ├── og.zma.osa.rda ├── osa.se.rda ├── zma.interpro.rda ├── zma.se.rda └── zma.tfs.rda ├── inst ├── CITATION ├── _pkgdown.yml ├── extdata │ └── Orthogroups.tsv └── script │ └── README.md ├── man ├── BioNERO-package.Rd ├── PC_correction.Rd ├── SFT_fit.Rd ├── ZKfiltering.Rd ├── check_SFT.Rd ├── consensus_SFT_fit.Rd ├── consensus_modules.Rd ├── consensus_trait_cor.Rd ├── cor2adj.Rd ├── cormat_to_edgelist.Rd ├── detect_communities.Rd ├── dfs2one.Rd ├── enrichment_analysis.Rd ├── exp2cor.Rd ├── exp2gcn.Rd ├── exp2gcn_blockwise.Rd ├── exp2grn.Rd ├── exp_genes2orthogroups.Rd ├── exp_preprocess.Rd ├── figures │ └── logo.png ├── filt.se.Rd ├── filter_by_variance.Rd ├── gene_significance.Rd ├── get_HK.Rd ├── get_edge_list.Rd ├── get_hubs_gcn.Rd ├── get_hubs_grn.Rd ├── get_neighbors.Rd ├── grn_average_rank.Rd ├── grn_combined.Rd ├── grn_filter.Rd ├── grn_infer.Rd ├── is_singleton.Rd ├── modPres_WGCNA.Rd ├── modPres_netrep.Rd ├── module_enrichment.Rd ├── module_preservation.Rd ├── module_stability.Rd ├── module_trait_cor.Rd ├── net_stats.Rd ├── og.zma.osa.Rd ├── osa.se.Rd ├── parse_orthofinder.Rd ├── plot_PCA.Rd ├── plot_dendro_and_colors.Rd ├── plot_eigengene_network.Rd ├── plot_expression_profile.Rd ├── plot_gcn.Rd ├── plot_gene_significance.Rd ├── plot_grn.Rd ├── plot_heatmap.Rd ├── plot_module_trait_cor.Rd ├── plot_ngenes_per_module.Rd ├── plot_ppi.Rd ├── q_normalize.Rd ├── remove_nonexp.Rd ├── replace_na.Rd ├── zma.interpro.Rd ├── zma.se.Rd └── zma.tfs.Rd ├── tests ├── testthat.R └── testthat │ ├── test_comparison.R │ ├── test_consensusmodules.R │ ├── test_data_preprocess.R │ ├── test_evolutionary.R │ ├── test_exploratory_analyses.R │ ├── test_gcn.R │ ├── test_grn.R │ ├── test_stats.R │ ├── test_utils.R │ └── test_visualization.R └── vignettes ├── vignette1.bib ├── vignette2.bib ├── vignette3.bib ├── vignette_01_GCN_inference.Rmd ├── vignette_02_GRN_inference.Rmd └── vignette_03_network_comparison.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/almeidasilvaf/BioNERO/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | -------------------------------------------------------------------------------- /.github/workflows/check-bioc.yml: -------------------------------------------------------------------------------- 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