| abiotic_stresses | Combined abiotic stresses |
| aggregate_splice_variants | Aggregate splice variants |
| app_ui | The application User-Interface |
| are_splice_variants | Are splice variants |
| check_IDs | Check compatibility between gene IDs and an organism |
| community_structure | Returns modules-communities memberships |
| convert_from_agi | For A. thaliana, converts TAIR IDs to entrez IDs, gene symbol... |
| convert_from_ensembl | For H. sapiens, converts ensembl IDs to entrez IDs, symbol or... |
| convert_from_ensembl_ce | For C. elegans, converts ensembl IDs to entrez IDs, symbol or... |
| convert_from_ensembl_dm | For D. melanogaster, converts ensembl IDs to entrez IDs,... |
| convert_from_ensembl_eck12 | For E coli, converts ensembl IDs to entrez IDs, symbol or... |
| convert_from_ensembl_mus | For M. musculus, converts ensembl IDs to entrez IDs, symbol... |
| describe_node | Targets and regulators of a gene in a network |
| draw_coseq_run | Displays clustering results and quality |
| draw_DEGs | MA or volcano plot for differential expression results |
| draw_discarded_edges | Draw network with removed edges in red |
| draw_distributions | Draw distributions of expression data |
| draw_enrich_go | Plot the enriched go terms of an enrich_go result |
| draw_enrich_go_map | Draw GO enrichment map |
| draw_expression_levels | Draw gene expression levels |
| draw_glm | Plots the coefficients value of a Poisson generalized linear... |
| draw_heatmap | Draw expression heatmap |
| draw_network | Interactive network view |
| draw_network_degrees | Draw a network's degree distributions |
| draw_PCA | Draw PCA results |
| draw_profiles | Draw expression profiles of a clustering |
| draw_venn | Venn diagram |
| enrich_go | Enriched ontologies for recognized organisms |
| enrich_go_custom | Enriched ontologies for a custom organism |
| estimateDEGs | Estimates Differentially Expression Genes |
| estimateDispersion | Estimates gene dispersions prior to differential expression... |
| estimate_test_edges_time | Estimates time spent for statistical testing |
| filter_low_counts | Remove low count genes |
| fit_glm | Fits a Poisson generalized linear model to a set of genes |
| gene_annotations | Gene annotations for supported organisms in DIANE |
| GENIE3OOB | GENIE3OOB |
| get_correlation | Get correlation |
| get_factors_from_conditions | Returns the factors that don't stay at the same level between... |
| get_gene_information | Get genes information |
| get_genes_in_cluster | Get genes in a specific cluster |
| get_locus | Get gene IDs loci, without splicing information |
| get_nEdges | Get the number of a edges in a graph, given a desired density |
| group_regressors | Group correlated regulators |
| interGO | Number of shared genes between Two GO terms |
| network_data | Creates data describing a gene regulatory network |
| network_from_tests | Create network from edges statistical tests |
| network_inference | Regulatory importances estimation via Random Forests |
| network_thresholding | Thresholds a non sparse adjascency matrix to return the... |
| normalize | Normalize raw count data |
| regulators_per_organism | List of regulator genes for a number of model organisms |
| run_app | Run the Shiny Application |
| run_coseq | Mixture Model clustering |
| test_edges | Statistical edges testing by permutations |
