Package: GeneTonic 3.1.0

Federico Marini

GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

This package provides functionality to combine the existing pieces of the transcriptome data and results, making it easier to generate insightful observations and hypothesis. Its usage is made easy with a Shiny application, combining the benefits of interactivity and reproducibility e.g. by capturing the features and gene sets of interest highlighted during the live session, and creating an HTML report as an artifact where text, code, and output coexist. Using the GeneTonicList as a standardized container for all the required components, it is possible to simplify the generation of multiple visualizations and summaries.

Authors:Federico Marini [aut, cre], Annekathrin Ludt [aut]

GeneTonic_3.1.0.tar.gz
GeneTonic_3.1.0.zip(r-4.5)GeneTonic_3.1.0.zip(r-4.4)GeneTonic_2.99.1.zip(r-4.3)
GeneTonic_3.1.0.tgz(r-4.4-any)GeneTonic_2.99.1.tgz(r-4.3-any)
GeneTonic_3.1.0.tar.gz(r-4.5-noble)GeneTonic_3.1.0.tar.gz(r-4.4-noble)
GeneTonic_3.1.0.tgz(r-4.4-emscripten)GeneTonic_2.99.1.tgz(r-4.3-emscripten)
GeneTonic.pdf |GeneTonic.html✨
GeneTonic/json (API)
NEWS

# Install 'GeneTonic' in R:
install.packages('GeneTonic', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/federicomarini/genetonic/issues

Datasets:

On BioConductor:GeneTonic-2.99.1(bioc 3.20)GeneTonic-2.8.0(bioc 3.19)

guigeneexpressionsoftwaretranscriptiontranscriptomicsvisualizationdifferentialexpressionpathwaysreportwritinggenesetenrichmentannotationgoshinyappsbioconductorbioconductor-packagedata-explorationdata-visualizationfunctional-enrichment-analysisgene-expressionpathway-analysisreproducible-researchrna-seq-analysisrna-seq-datashinytranscriptomeuser-friendly

8.18 score 76 stars 1 packages 37 scripts 538 downloads 1 mentions 55 exports 209 dependencies

Last updated 23 days agofrom:eae9a0325e. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 07 2024
R-4.3-macOKOct 07 2024

Exports:check_colorscheckup_GeneToniccheckup_gtlcluster_markovcreate_jaccard_matrixcreate_kappa_matrixcreate_upsetdatadescribe_gtldeseqresult2dfdistill_enrichmentenhance_tableenrichment_mapexport_for_iSEEexport_to_sifgene_plotgeneinfo_2_htmlGeneTonicGeneTonic_listGeneTonicListget_aggrscoresget_expression_valuesggs_backboneggs_graphgo_2_htmlgs_alluvialgs_dendrogs_fuzzyclusteringgs_heatmapgs_horizongs_mdsgs_radargs_sankeygs_scoresgs_scoresheatgs_simplifygs_spidergs_summary_heatgs_summary_overviewgs_summary_overview_pairgs_upsetgs_volcanohappy_hourmap2coloroverlap_coefficientoverlap_jaccard_indexshake_davidResultshake_enrichResultshake_enrichrResultshake_fgseaResultshake_gprofilerResultshake_gsenrichResultshake_topGOtableResultsignature_volcanostyleColorBar_divergentsummarize_ggs_hubgenes

Dependencies:abindAnnotationDbiapeaplotaskpassbackbonebase64encBHBiasedUrnBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobbs4DashbslibcachemcirclizecliclueclusterclusterProfilercodetoolscolorspacecolourpickercommonmarkComplexHeatmapComplexUpsetcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydendextendDESeq2digestdoParallelDOSEdplyrDTdynamicTreeCutenrichplotevaluateexpmfansifarverfastmapfastmatchfgseafilelockfontawesomeforeachformatRfreshfsfutile.loggerfutile.optionsgeneLenDataBasegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggforceggfunggnewscaleggplot2ggplotifyggrepelggridgesggtangleggtreeGlobalOptionsglueGO.dbGOSemSimgoseqgraphgridExtragridGraphicsgsongtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImosdefmunsellnlmeopensslpatchworkpillarpkgconfigplogrplotlyplyrpngpolyclipprettyunitsprogresspromisespurrrqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreshape2restfulrRhtslibrintrojsrjsonrlangrmarkdownRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalesscatterpieshapeshinyshinyAceshinycssloadersshinyjsshinyWidgetssnowsourcetoolsSparseArraySparseMstringistringrSummarizedExperimentsyssystemfontstibbletidyrtidyselecttidytreetinytextippytopGOtreeiotweenrtxdbmakerUCSC.utilsutf8vctrsviridisviridisLitevisNetworkwaiterwithrxfunXMLxml2xtableXVectoryamlyulab.utilszlibbioc

The GeneTonic User's Guide

Federico Marini, Annekathrin Ludt

Rendered fromGeneTonic_manual.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-09-22
Started: 2019-06-24

Readme and manuals

Help Manual

Help pageTopics
Check whether 'pandoc' and 'pandoc-citeproc' are available.check_pandoc
Check colorscheck_colors
Checking the input objects for GeneToniccheckup_GeneTonic
Checking the 'gtl' input object for GeneToniccheckup_gtl
Markov Clustering (MCL) for community detectioncluster_markov
Compute the overlap matrix for enrichment resultscreate_jaccard_matrix
Compute the kappa matrix for enrichment resultscreate_kappa_matrix
Create a geneset upset datasetcreate_upsetdata
Deprecated functions in GeneTonicdeprecated
Describe a GeneTonic listdescribe_gtl
Generate a table from the 'DESeq2' resultsdeseqresult2df
Distill enrichment resultsdistill_enrichment
Extract vectors from editor contenteditor_to_vector_sanitized
Visually enhances a functional enrichment result tableenhance_table
Creates an enrichment map for the results of functional enrichmentenrichment_map
A sample output from Enrichrenrichr_output_macrophage
export_for_iSEEexport_for_iSEE
Export to sifexport_to_sif
A sample output from fgseafgseaRes
Plot expression values for a genegene_plot
Information on a genegeneinfo_2_html
GeneTonicGeneTonic
Create a GeneTonicList objectGeneTonicList GeneTonic_list
Compute aggregated scores for gene setsget_aggrscores
Get expression valuesget_expression_values
Extract the backbone for the gene-geneset graphggs_backbone
Construct a gene-geneset-graphggs_graph
Information on a GeneOntology identifiergo_2_html
A sample output from g:Profilergostres_macrophage
Alluvial (sankey) plot for a set of genesets and the associated genesgs_alluvial gs_sankey
Dendrogram of the gene set enrichment resultsgs_dendro
Compute fuzzy clusters of gene setsgs_fuzzyclustering
Plot a heatmap of the gene signature on the datags_heatmap
Plots a summary of enrichment resultsgs_horizon
Multi Dimensional Scaling plot for gene setsgs_mds
Radar (spider) plot for gene setsgs_radar gs_spider
Compute gene set scoresgs_scores
Plots a matrix of geneset scoresgs_scoresheat
Simplify results from functional enrichment analysisgs_simplify
Plots a heatmap for genes and genesetsgs_summary_heat
Plots a summary of enrichment resultsgs_summary_overview
Plots a summary of enrichment resultsgs_summary_overview_pair
Upset plot for genesetsgs_upset
Volcano plot for gene setsgs_volcano
Happy hour!happy_hour
Maps numeric values to color valuesmap2color
Calculate overlap coefficientoverlap_coefficient
Calculate Jaccard Index between two setsoverlap_jaccard_index
A sample 'DESeqResults' objectres_macrophage_IFNg_vs_naive
Convert the output of DAVIDshake_davidResult
Convert an enrichResult objectshake_enrichResult
Convert the output of Enrichrshake_enrichrResult
Convert the output of fgseashake_fgseaResult
Convert the output of g:Profilershake_gprofilerResult
Convert a gseaResult objectshake_gsenrichResult
Convert a topGOtableResult objectshake_topGOtableResult
Plot a volcano plot of a genesetsignature_volcano
Style DT color barsstyleColorBar_divergent
Summarize information on the hub genessummarize_ggs_hubgenes
A sample 'res_enrich' objecttopgoDE_macrophage_IFNg_vs_naive