Package: ReactomeGSA 1.21.0
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:
ReactomeGSA_1.21.0.tar.gz
ReactomeGSA_1.21.0.zip(r-4.5)ReactomeGSA_1.21.0.zip(r-4.4)ReactomeGSA_1.21.0.zip(r-4.3)
ReactomeGSA_1.21.0.tgz(r-4.4-any)ReactomeGSA_1.21.0.tgz(r-4.3-any)
ReactomeGSA_1.21.0.tar.gz(r-4.5-noble)ReactomeGSA_1.21.0.tar.gz(r-4.4-noble)
ReactomeGSA_1.21.0.tgz(r-4.4-emscripten)ReactomeGSA_1.21.0.tgz(r-4.3-emscripten)
ReactomeGSA.pdf |ReactomeGSA.html✨
ReactomeGSA/json (API)
NEWS
| # 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-1.21.0(bioc 3.21)ReactomeGSA-1.20.0(bioc 3.20)
genesetenrichmentproteomicstranscriptomicssystemsbiologygeneexpressionreactome
Last updated 23 days agofrom:3152a83a33. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:add_datasetanalyse_sc_clustersfind_public_datasetsget_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:askpassBiobaseBiocGenericsbitopscaToolsclicolorspacecpp11crayoncurldplyrfansifarvergenericsggplot2gluegplotsgtablegtoolshmshttrisobandjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerrlangscalesstringistringrsystibbletidyrtidyselectutf8vctrsviridisLitewithr
Analysing single-cell RNA-sequencing Data
Rendered fromanalysing-scRNAseq.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2023-11-12
Started: 2020-04-11
Loading and re-analysing public data through ReactomeGSA
Rendered fromreanalysing-public-data.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2024-02-01
Started: 2023-11-28
Using the ReactomeGSA package
Rendered fromusing-reactomegsa.Rmdusingknitr::rmarkdownon Oct 31 2024.Last update: 2023-11-12
Started: 2019-07-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| add_dataset | add_dataset |
| add_dataset - data.frame | add_dataset,ReactomeAnalysisRequest,data.frame-method |
| add_dataset - DGEList | add_dataset,ReactomeAnalysisRequest,DGEList-method |
| add_dataset - EList | add_dataset,ReactomeAnalysisRequest,EList-method |
| add_dataset - ExpressionSet | add_dataset,ReactomeAnalysisRequest,ExpressionSet-method |
| add_dataset - matrix | add_dataset,ReactomeAnalysisRequest,matrix-method |
| analyse_sc_clusters | analyse_sc_clusters |
| analyse_sc_clusters - Seurat | analyse_sc_clusters,Seurat-method |
| analyse_sc_clusters - SingleCellExperiment | analyse_sc_clusters,SingleCellExperiment-method |
| break_names | break_names |
| check_reactome_url | check_reactome_url |
| Check's if a ReactomeAnalysisRequest object is valid | checkRequestValidity |
| Convert the Reactome JSON result to a ReactomeAnalysisResult object | convert_reactome_result |
| Converts a data.frame to a string representation | data_frame_as_string |
| fetch_public_data | fetch_public_data |
| find_public_datasets | find_public_datasets |
| Retrieves the status of the submitted dataset loading request | get_dataset_loading_status |
| get_fc_for_dataset | get_fc_for_dataset |
| get_is_sig_dataset | get_is_sig_dataset |
| get_public_species | get_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 types | get_reactome_data_types |
| get_reactome_methods | get_reactome_methods |
| get_result | get_result |
| ReactomeAnalysisResult - get_result | get_result,ReactomeAnalysisResult-method |
| is_gsva_result | is_gsva_result |
| load_public_dataset | load_public_dataset |
| ReactomeAnalysisResult - names | names,ReactomeAnalysisResult-method |
| open_reactome | open_reactome |
| open_reactome - ReactomeAnalysisResult | open_reactome,ReactomeAnalysisResult-method |
| pathways | pathways |
| ReactomeAnalysisResult - pathways | pathways,ReactomeAnalysisResult-method |
| Perform a Reactome Analaysis | perform_reactome_analysis |
| plot_correlations | plot_correlations |
| plot_correlations - ReactomeAnalysisResult | plot_correlations,ReactomeAnalysisResult-method |
| plot_gsva_heatmap | plot_gsva_heatmap |
| plot_gsva_heatmap - ReactomeAnalysisResult function | plot_gsva_heatmap,ReactomeAnalysisResult-method |
| plot_gsva_pathway | plot_gsva_pathway |
| ReactomeAnalysisResult - plot_gsva_pathway | plot_gsva_pathway,ReactomeAnalysisResult-method |
| plot_gsva_pca | plot_gsva_pca |
| plot_gsva_pca - ReactomeAnalysisResult | plot_gsva_pca,ReactomeAnalysisResult-method |
| plot_heatmap | plot_heatmap |
| plot_heatmap - ReactomeAnalysisResult | plot_heatmap,ReactomeAnalysisResult-method |
| plot_volcano | plot_volcano |
| ReactomeAnalysisResult - plot_volcano | plot_volcano,ReactomeAnalysisResult-method |
| print - ReactomeAnalysisRequest | print,ReactomeAnalysisRequest-method |
| print - ReactomeAnalysisResult | print,ReactomeAnalysisResult-method |
| reactome_links | reactome_links |
| ReactomeAnalysisResult - reactome_links | reactome_links,ReactomeAnalysisResult-method |
| ReactomeAnalysisRequest class | ReactomeAnalysisRequest |
| ReactomeAnalysisResult class | ReactomeAnalysisResult ReactomeAnalysisResult-class |
| remove_dataset | remove_dataset |
| remove_dataset - ReactomeAnalysisRequest | remove_dataset,ReactomeAnalysisRequest-method |
| result_types | result_types |
| ReactomeAnalysisResult - result_types | result_types,ReactomeAnalysisResult-method |
| set_method | set_method |
| set_method - ReactomeAnalysisRequest | set_method,ReactomeAnalysisRequest-method |
| set_parameters | set_parameters |
| ReactomeAnalysisRequest - set_parameters | set_parameters,ReactomeAnalysisRequest-method |
| print - ReactomeAnalysisRequest | show,ReactomeAnalysisRequest-method |
| show - ReactomeAnalysisResult | show,ReactomeAnalysisResult-method |
| Start Reactome Analysis | start_reactome_analysis |
| wait_for_loading_dataset | wait_for_loading_dataset |