Client for the Reactome Analysis Service for comparative
multi-omics gene set analysis
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Documentation for package ‘ReactomeGSA’ version 1.18.0
Help Pages
| add_dataset | add_dataset |
| add_dataset-method | add_dataset - DGEList |
| add_dataset-method | add_dataset - EList |
| add_dataset-method | add_dataset - ExpressionSet |
| add_dataset-method | add_dataset - data.frame |
| add_dataset-method | add_dataset - matrix |
| analyse_sc_clusters | analyse_sc_clusters |
| analyse_sc_clusters-method | analyse_sc_clusters - Seurat |
| analyse_sc_clusters-method | analyse_sc_clusters - SingleCellExperiment |
| break_names | break_names |
| checkRequestValidity | Check's if a ReactomeAnalysisRequest object is valid |
| check_reactome_url | check_reactome_url |
| convert_reactome_result | Convert the Reactome JSON result to a ReactomeAnalysisResult object |
| data_frame_as_string | Converts a data.frame to a string representation |
| fetch_public_data | fetch_public_data |
| find_public_datasets | find_public_datasets |
| get_dataset_loading_status | Retrieves the status of the submitted dataset loading request |
| get_fc_for_dataset | get_fc_for_dataset |
| get_is_sig_dataset | get_is_sig_dataset |
| get_public_species | get_public_species |
| get_reactome_analysis_result | Retrieves the result of the submitted analysis using 'perform_reactome_analysis' |
| get_reactome_analysis_status | Retrieves the status of the submitted analysis using 'start_reactome_analysis' |
| get_reactome_data_types | ReactomeGSA supported data types |
| get_reactome_methods | get_reactome_methods |
| get_result | get_result |
| get_result-method | ReactomeAnalysisResult - get_result |
| is_gsva_result | is_gsva_result |
| load_public_dataset | load_public_dataset |
| names-method | ReactomeAnalysisResult - names |
| open_reactome | open_reactome |
| open_reactome-method | open_reactome - ReactomeAnalysisResult |
| pathways | pathways |
| pathways-method | ReactomeAnalysisResult - pathways |
| perform_reactome_analysis | Perform a Reactome Analaysis |
| plot_correlations | plot_correlations |
| plot_correlations-method | plot_correlations - ReactomeAnalysisResult |
| plot_gsva_heatmap | plot_gsva_heatmap |
| plot_gsva_heatmap-method | plot_gsva_heatmap - ReactomeAnalysisResult function |
| plot_gsva_pathway | plot_gsva_pathway |
| plot_gsva_pathway-method | ReactomeAnalysisResult - plot_gsva_pathway |
| plot_gsva_pca | plot_gsva_pca |
| plot_gsva_pca-method | plot_gsva_pca - ReactomeAnalysisResult |
| plot_heatmap | plot_heatmap |
| plot_heatmap-method | plot_heatmap - ReactomeAnalysisResult |
| plot_volcano | plot_volcano |
| plot_volcano-method | ReactomeAnalysisResult - plot_volcano |
| print-method | print - ReactomeAnalysisRequest |
| print-method | print - ReactomeAnalysisResult |
| ReactomeAnalysisRequest | ReactomeAnalysisRequest class |
| ReactomeAnalysisResult | ReactomeAnalysisResult class |
| ReactomeAnalysisResult-class | ReactomeAnalysisResult class |
| reactome_links | reactome_links |
| reactome_links-method | ReactomeAnalysisResult - reactome_links |
| remove_dataset | remove_dataset |
| remove_dataset-method | remove_dataset - ReactomeAnalysisRequest |
| result_types | result_types |
| result_types-method | ReactomeAnalysisResult - result_types |
| set_method | set_method |
| set_method-method | set_method - ReactomeAnalysisRequest |
| set_parameters | set_parameters |
| set_parameters-method | ReactomeAnalysisRequest - set_parameters |
| show-method | print - ReactomeAnalysisRequest |
| show-method | show - ReactomeAnalysisResult |
| start_reactome_analysis | Start Reactome Analysis |
| wait_for_loading_dataset | wait_for_loading_dataset |