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

## Documentation for package ‘ReactomeGSA’ version 1.25.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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
generate_metadata | generate_metadata
generate_metadata-method | Generate metadata
generate_pseudo_bulk_data | generate_pseudo_bulk_data
generate_pseudo_bulk_data-method | generate_pseudo_bulk_data - Seurat
generate_pseudo_bulk_data-method | generate_pseudo_bulk_data - SingleCellExperiment
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
split_clustering | method implementation subclustering
split_random_sce | split SCE Object with random pooling
split_subclustering_sce | split SCE Object with random pooling
split_variable | split Seurat object by variable
split_variable_random | split Seurat object by random pooling
split_variable_sce | split SCE Object by variable
start_reactome_analysis | Start Reactome Analysis
wait_for_loading_dataset | wait_for_loading_dataset