Enjoy Analyzing And Integrating The Results From Differential
Expression Analysis And Functional Enrichment Analysis
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Documentation for package ‘GeneTonic’ version 3.3.2
Help Pages
| .check_pandoc | Check whether 'pandoc' and 'pandoc-citeproc' are available |
| checkup_GeneTonic | Checking the input objects for GeneTonic |
| checkup_gtl | Checking the 'gtl' input object for GeneTonic |
| check_colors | Check colors |
| cluster_markov | Markov Clustering (MCL) for community detection |
| create_jaccard_matrix | Compute the overlap matrix for enrichment results |
| create_kappa_matrix | Compute the kappa matrix for enrichment results |
| create_upsetdata | Create a geneset upset dataset |
| deprecated | Deprecated functions in GeneTonic |
| describe_gtl | Describe a GeneTonic list |
| deseqresult2df | Generate a table from the 'DESeq2' results |
| distill_enrichment | Distill enrichment results |
| editor_to_vector_sanitized | Extract vectors from editor content |
| enhance_table | Visually enhances a functional enrichment result table |
| enrichment_map | Creates an enrichment map for the results of functional enrichment |
| enrichr_output_macrophage | A sample output from Enrichr |
| export_for_iSEE | export_for_iSEE |
| export_to_sif | Export to sif |
| fgseaRes | A sample output from fgsea |
| geneinfo_2_html | Information on a gene |
| GeneTonic | GeneTonic |
| GeneTonicList | Create a GeneTonicList object |
| GeneTonic_list | Create a GeneTonicList object |
| gene_plot | Plot expression values for a gene |
| get_aggrscores | Compute aggregated scores for gene sets |
| get_expression_values | Get expression values |
| ggs_backbone | Extract the backbone for the gene-geneset graph |
| ggs_graph | Construct a gene-geneset-graph |
| gostres_macrophage | A sample output from g:Profiler |
| go_2_html | Information on a GeneOntology identifier |
| gs_alluvial | Alluvial (sankey) plot for a set of genesets and the associated genes |
| gs_dendro | Dendrogram of the gene set enrichment results |
| gs_fuzzyclustering | Compute fuzzy clusters of gene sets |
| gs_heatmap | Plot a heatmap of the gene signature on the data |
| gs_horizon | Plots a summary of enrichment results |
| gs_mds | Multi Dimensional Scaling plot for gene sets |
| gs_radar | Radar (spider) plot for gene sets |
| gs_sankey | Alluvial (sankey) plot for a set of genesets and the associated genes |
| gs_scores | Compute gene set scores |
| gs_scoresheat | Plots a matrix of geneset scores |
| gs_simplify | Simplify results from functional enrichment analysis |
| gs_spider | Radar (spider) plot for gene sets |
| gs_summary_heat | Plots a heatmap for genes and genesets |
| gs_summary_overview | Plots a summary of enrichment results |
| gs_summary_overview_pair | Plots a summary of enrichment results |
| gs_upset | Upset plot for genesets |
| gs_volcano | Volcano plot for gene sets |
| happy_hour | Happy hour! |
| map2color | Maps numeric values to color values |
| overlap_coefficient | Calculate overlap coefficient |
| overlap_jaccard_index | Calculate Jaccard Index between two sets |
| res_macrophage_IFNg_vs_naive | A sample 'DESeqResults' object |
| shake_davidResult | Convert the output of DAVID |
| shake_enrichResult | Convert an enrichResult object |
| shake_enrichrResult | Convert the output of Enrichr |
| shake_fgseaResult | Convert the output of fgsea |
| shake_gprofilerResult | Convert the output of g:Profiler |
| shake_gsenrichResult | Convert a gseaResult object |
| shake_topGOtableResult | Convert a topGOtableResult object |
| signature_volcano | Plot a volcano plot of a geneset |
| styleColorBar_divergent | Style DT color bars |
| summarize_ggs_hubgenes | Summarize information on the hub genes |
| topgoDE_macrophage_IFNg_vs_naive | A sample 'res_enrich' object |