Package: GeneTonic 3.7.0

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 Nedwed [aut], Edoardo Filippi [ctb]

GeneTonic_3.7.0.tar.gz
GeneTonic_3.7.0.zip(r-4.7)GeneTonic_3.7.0.zip(r-4.6)GeneTonic_3.7.0.zip(r-4.5)
GeneTonic_3.7.0.tgz(r-4.6-any)GeneTonic_3.7.0.tgz(r-4.5-any)
GeneTonic_3.7.0.tar.gz(r-4.7-any)GeneTonic_3.7.0.tar.gz(r-4.6-any)
GeneTonic_3.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GeneTonic/json (API)

# Install 'GeneTonic' in R:

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

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

Datasets:

enrichr_output_macrophage - A sample output from Enrichr
fgseaRes - A sample output from fgsea
gostres_macrophage - A sample output from g:Profiler
res_macrophage_IFNg_vs_naive - A sample 'DESeqResults' object
topgoDE_macrophage_IFNg_vs_naive - A sample 'res_enrich' object

On BioConductor:GeneTonic-3.7.0(bioc 3.24)GeneTonic-3.6.0(bioc 3.23)

gui geneexpression software transcription transcriptomics visualization differentialexpression pathways reportwriting genesetenrichment annotation go shinyapps bioconductor bioconductor-package data-exploration data-visualization functional-enrichment-analysis gene-expression pathway-analysis reproducible-research rna-seq-analysis rna-seq-data shiny transcriptome user-friendly

8.10 score 84 stars 1 packages 55 scripts 464 downloads 1 mentions 55 exports 213 dependencies

Last updated from:d2ad76fbe2. Checks:1 WARNING, 8 OK, 1 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	329
linux-devel-x86_64	OK	874
source / vignettes	OK	536
linux-release-x86_64	OK	868
macos-release-arm64	OK	697
macos-oldrel-arm64	ERROR	666
windows-devel	OK	944
windows-release	OK	891
windows-oldrel	OK	699
wasm-release	OK	292

Exports:check_colors checkup_GeneTonic checkup_gtl cluster_markov create_jaccard_matrix create_kappa_matrix create_upsetdata describe_gtl deseqresult2df distill_enrichment enhance_table enrichment_map export_for_iSEE export_to_sif gene_plot geneinfo_2_html GeneTonic GeneTonic_list GeneTonicList get_aggrscores get_expression_values ggs_backbone ggs_graph go_2_html gs_alluvial gs_dendro gs_fuzzyclustering gs_heatmap gs_horizon gs_mds gs_radar gs_sankey gs_scores gs_scoresheat gs_simplify gs_spider gs_summary_heat gs_summary_overview gs_summary_overview_pair gs_upset gs_volcano happy_hour map2color overlap_coefficient overlap_jaccard_index shake_davidResult shake_enrichResult shake_enrichrResult shake_fgseaResult shake_gprofilerResult shake_gsenrichResult shake_topGOtableResult signature_volcano styleColorBar_divergent summarize_ggs_hubgenes

Dependencies:abind aisdk AnnotationDbi ape aplot askpass backbone base64enc BH BiasedUrn Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob bs4Dash bslib cachem callr cigarillo circlize cli clue cluster clusterProfiler codetools colorspace colourpicker commonmark ComplexHeatmap ComplexUpset cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray dendextend DESeq2 digest doParallel DOSE dplyr DT dynamicTreeCut enrichit enrichplot evaluate expm farver fastmap filelock fontawesome fontBitstreamVera fontLiberation fontquiver foreach formatR fresh fs futile.logger futile.options gdtools geneLenDataBase generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggridges ggtangle ggtree GlobalOptions glue GO.db GOSemSim goseq graph gridExtra gridGraphics gson gtable highr hms htmltools htmlwidgets httpuv httr httr2 igraph IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI mosdef nlme openssl otel patchwork pillar pkgconfig plotly plyr png polyclip prettyunits processx progress promises ps purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl reshape2 restfulr Rhtslib rintrojs rjson rlang rmarkdown Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales scatterpie Seqinfo shape shiny shinyAce shinycssloaders shinyjs shinyWidgets snow sourcetools SparseArray SparseM stringi stringr SummarizedExperiment sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex tippy topGO treeio tweenr txdbmaker UCSC.utils utf8 vctrs viridis viridisLite visNetwork waiter withr xfun XML xml2 xtable XVector yaml yulab.utils

The GeneTonic User's Guide

Rendered fromGeneTonic_manual.Rmdusingknitr::rmarkdown

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

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

Package: GeneTonic 3.7.0

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

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