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


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Documentation for package ‘ReactomeGSA’ version 1.12.0

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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
get_fc_for_dataset get_fc_for_dataset
get_is_sig_dataset get_is_sig_dataset
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
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