Man pages for GeneTonic
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

check_colorsCheck colors
checkup_GeneTonicChecking the input objects for GeneTonic
cluster_markovMarkov Clustering (MCL) for community detection
create_jaccard_matrixCompute the overlap matrix for enrichment results
create_kappa_matrixCompute the kappa matrix for enrichment results
deseqresult2dfGenerate a table from the 'DESeq2' results
distill_enrichmentDistill enrichment results
dot-check_pandocCheck whether 'pandoc' and 'pandoc-citeproc' are available
enhance_tableVisually enhances a functional enrichment result table
enrichment_mapCreates an enrichment map for the results of functional...
enrichr_output_macrophageA sample output from Enrichr
export_to_sifExport to sif
fgseaResA sample output from fgsea
geneinfo_2_htmlInformation on a gene
gene_plotPlot expression values for a gene
get_aggrscoresCompute aggregated scores for gene sets
get_expression_valuesGet expression values
ggs_graphConstruct a gene-geneset-graph
go_2_htmlInformation on a GeneOntology identifier
gostres_macrophageA sample output from g:Profiler
gs_alluvialAlluvial (sankey) plot for a set of genesets and the...
gs_dendroDendrogram of the gene set enrichment results
gs_heatmapPlot a heatmap of the gene signature on the data
gs_horizonPlots a summary of enrichment results
gs_mdsMulti Dimensional Scaling plot for gene sets
gs_radarRadar (spider) plot for gene sets
gs_scoresCompute gene set scores
gs_scoresheatPlots a matrix of geneset scores
gs_simplifySimplify results from functional enrichment analysis
gs_summary_heatPlots a heatmap for genes and genesets
gs_summary_overviewPlots a summary of enrichment results
gs_summary_overview_pairPlots a summary of enrichment results
gs_volcanoVolcano plot for gene sets
happy_hourHappy hour!
map2colorMaps numeric values to color values
overlap_coefficientCalculate overlap coefficient
overlap_jaccard_indexCalculate Jaccard Index between two sets
res_macrophage_IFNg_vs_naiveA sample 'DESeqResults' object
shake_davidResultConvert the output of DAVID
shake_enrichResultConvert an enrichResult object
shake_enrichrResultConvert the output of Enrichr
shake_fgseaResultConvert the output of fgsea
shake_gprofilerResultConvert the output of g:Profiler
shake_topGOtableResultConvert a topGOtableResult object
styleColorBar_divergentStyle DT color bars
topgoDE_macrophage_IFNg_vs_naiveA sample 'res_enrich' object
GeneTonic documentation built on Nov. 8, 2020, 5:27 p.m.