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

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Documentation for package ‘ReactomeGSA’ version 1.21.2

• 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