Package: ReactomeGSA 1.27.2

Johannes Griss

ReactomeGSA: Client for the Reactome Analysis Service for comparative multi-omics gene set analysis

The ReactomeGSA packages uses Reactome's online analysis service to perform a multi-omics gene set analysis. The main advantage of this package is, that the retrieved results can be visualized using REACTOME's powerful webapplication. Since Reactome's analysis service also uses R to perfrom the actual gene set analysis you will get similar results when using the same packages (such as limma and edgeR) locally. Therefore, if you only require a gene set analysis, different packages are more suited.

Authors:Johannes Griss [aut, cre]

ReactomeGSA_1.27.2.tar.gz
ReactomeGSA_1.27.2.zip(r-4.7)ReactomeGSA_1.27.2.zip(r-4.6)ReactomeGSA_1.27.2.zip(r-4.5)
ReactomeGSA_1.27.2.tgz(r-4.6-any)ReactomeGSA_1.27.2.tgz(r-4.5-any)
ReactomeGSA_1.27.2.tar.gz(r-4.7-any)ReactomeGSA_1.27.2.tar.gz(r-4.6-any)
ReactomeGSA_1.27.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ReactomeGSA/json (API)

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

Bug tracker:https://github.com/reactome/reactomegsa/issues

On BioConductor:ReactomeGSA-1.27.1(bioc 3.24)ReactomeGSA-1.26.0(bioc 3.23)

genesetenrichmentproteomicstranscriptomicssystemsbiologygeneexpressionreactome

8.71 score 33 stars 143 scripts 544 downloads 4 mentions 31 exports 77 dependencies

Last updated from:062cbf4d9d. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

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bioc-checksWARNING295
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source / vignettesOK537
linux-release-x86_64NOTE807
macos-release-arm64NOTE657
macos-oldrel-arm64NOTE739
windows-develNOTE1628
windows-releaseNOTE1742
windows-oldrelNOTE1324
wasm-releaseOK327

Exports:add_datasetanalyse_sc_clustersfind_public_datasetsgenerate_metadatagenerate_pseudo_bulk_dataget_public_speciesget_reactome_analysis_resultget_reactome_analysis_statusget_reactome_data_typesget_reactome_methodsget_resultload_public_datasetopen_reactomepathwaysperform_reactome_analysisplot_correlationsplot_gsva_heatmapplot_gsva_pathwayplot_gsva_pcaplot_heatmapplot_volcanoprintreactome_linksReactomeAnalysisRequestReactomeAnalysisResultremove_datasetresult_typesset_methodset_parametersshowstart_reactome_analysis

Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocGenericsBiocParallelBiocSingularbitopscaToolsclicodetoolscpp11crayoncurlDelayedArraydplyrfarverformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegplotsgtablegtoolshmshttrigraphIRangesirlbaisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcpprlangrsvdS4ArraysS4VectorsS7ScaledMatrixscalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrsviridisLitewithrXVector

Analysing single-cell RNA-sequencing Data
Introduction | Citation | Installation | Example data | Types of analyses | Comparative pathway analysis (pseudo-bulk approach) | Pathway analysis of cell clusters (analyse_sc_clusters) | Plotting the results | Pathway-level PCA | Session Info
Rendered fromanalysing-scRNAseq.Rmdusingknitr::rmarkdown

Last update: 2024-11-07
Started: 2020-04-11

Loading and re-analysing public data through ReactomeGSA
Introduction | Installation | Searching for Public Datasets | Load a public dataset | Perform the pathway analysis using ReactomeGSA | Session Info
Rendered fromreanalysing-public-data.Rmdusingknitr::rmarkdown

Last update: 2024-02-01
Started: 2023-11-28

Using the ReactomeGSA package
Introduction | Citation | Installation | Getting available methods | Creating an analysis request | Setting parameters | Adding datasets | Sample annotations | Name | Type | Defining the experimental design | Submitting the request | Investigating the result | Visualising results | Opening web-based visualization | Session Info
Rendered fromusing-reactomegsa.Rmdusingknitr::rmarkdown

Last update: 2023-11-12
Started: 2019-07-01

Readme and manuals

Help Manual

Help pageTopics
add_datasetadd_dataset
add_dataset - data.frameadd_dataset,ReactomeAnalysisRequest,data.frame-method
add_dataset - DGEListadd_dataset,ReactomeAnalysisRequest,DGEList-method
add_dataset - EListadd_dataset,ReactomeAnalysisRequest,EList-method
add_dataset - ExpressionSetadd_dataset,ReactomeAnalysisRequest,ExpressionSet-method
add_dataset - matrixadd_dataset,ReactomeAnalysisRequest,matrix-method
analyse_sc_clustersanalyse_sc_clusters
analyse_sc_clusters - Seuratanalyse_sc_clusters,Seurat-method
analyse_sc_clusters - SingleCellExperimentanalyse_sc_clusters,SingleCellExperiment-method
break_namesbreak_names
check_reactome_urlcheck_reactome_url
Check's if a ReactomeAnalysisRequest object is validcheckRequestValidity
Convert the Reactome JSON result to a ReactomeAnalysisResult objectconvert_reactome_result
Converts a data.frame to a string representationdata_frame_as_string
fetch_public_datafetch_public_data
find_public_datasetsfind_public_datasets
generate_metadatagenerate_metadata
Generate metadatagenerate_metadata,data.frame-method
generate_pseudo_bulk_datagenerate_pseudo_bulk_data
generate_pseudo_bulk_data - Seuratgenerate_pseudo_bulk_data,Seurat-method
generate_pseudo_bulk_data - SingleCellExperimentgenerate_pseudo_bulk_data,SingleCellExperiment-method
Retrieves the status of the submitted dataset loading requestget_dataset_loading_status
get_fc_for_datasetget_fc_for_dataset
get_is_sig_datasetget_is_sig_dataset
get_public_speciesget_public_species
Retrieves the result of the submitted analysis using 'perform_reactome_analysis'get_reactome_analysis_result
Retrieves the status of the submitted analysis using 'start_reactome_analysis'get_reactome_analysis_status
ReactomeGSA supported data typesget_reactome_data_types
get_reactome_methodsget_reactome_methods
get_resultget_result
ReactomeAnalysisResult - get_resultget_result,ReactomeAnalysisResult-method
is_gsva_resultis_gsva_result
load_public_datasetload_public_dataset
ReactomeAnalysisResult - namesnames,ReactomeAnalysisResult-method
open_reactomeopen_reactome
open_reactome - ReactomeAnalysisResultopen_reactome,ReactomeAnalysisResult-method
pathwayspathways
ReactomeAnalysisResult - pathwayspathways,ReactomeAnalysisResult-method
Perform a Reactome Analaysisperform_reactome_analysis
plot_correlationsplot_correlations
plot_correlations - ReactomeAnalysisResultplot_correlations,ReactomeAnalysisResult-method
plot_gsva_heatmapplot_gsva_heatmap
plot_gsva_heatmap - ReactomeAnalysisResult functionplot_gsva_heatmap,ReactomeAnalysisResult-method
plot_gsva_pathwayplot_gsva_pathway
ReactomeAnalysisResult - plot_gsva_pathwayplot_gsva_pathway,ReactomeAnalysisResult-method
plot_gsva_pcaplot_gsva_pca
plot_gsva_pca - ReactomeAnalysisResultplot_gsva_pca,ReactomeAnalysisResult-method
plot_heatmapplot_heatmap
plot_heatmap - ReactomeAnalysisResultplot_heatmap,ReactomeAnalysisResult-method
plot_volcanoplot_volcano
ReactomeAnalysisResult - plot_volcanoplot_volcano,ReactomeAnalysisResult-method
print - ReactomeAnalysisRequestprint,ReactomeAnalysisRequest-method
print - ReactomeAnalysisResultprint,ReactomeAnalysisResult-method
reactome_linksreactome_links
ReactomeAnalysisResult - reactome_linksreactome_links,ReactomeAnalysisResult-method
ReactomeAnalysisRequest classReactomeAnalysisRequest
ReactomeAnalysisResult classReactomeAnalysisResult ReactomeAnalysisResult-class
remove_datasetremove_dataset
remove_dataset - ReactomeAnalysisRequestremove_dataset,ReactomeAnalysisRequest-method
result_typesresult_types
ReactomeAnalysisResult - result_typesresult_types,ReactomeAnalysisResult-method
set_methodset_method
set_method - ReactomeAnalysisRequestset_method,ReactomeAnalysisRequest-method
set_parametersset_parameters
ReactomeAnalysisRequest - set_parametersset_parameters,ReactomeAnalysisRequest-method
print - ReactomeAnalysisRequestshow,ReactomeAnalysisRequest-method
show - ReactomeAnalysisResultshow,ReactomeAnalysisResult-method
method implementation subclusteringsplit_clustering
split SCE Object with random poolingsplit_random_sce
split SCE Object with random poolingsplit_subclustering_sce
split Seurat object by variablesplit_variable
split Seurat object by random poolingsplit_variable_random
split SCE Object by variablesplit_variable_sce
Start Reactome Analysisstart_reactome_analysis
wait_for_loading_datasetwait_for_loading_dataset