Download Different Reactome Analysis ResultsSource:
Based on the "request" argument, you can download different analysis results data associated with a given token.
A token associated to your previous Reactome analysis.
What to download? Should be one of:
"found_ids": Download a CSV file containing the found user-supplied identifiers in the analysis associated with your supplied token and resource.
"not_found_ids"" Download a CSV file containing the user-supplied Identifiers which has not been found in the analysis associated with your supplied token.
"pathways": Download a CSV file containing Pathway analysis results of the analysis associated with your supplied token and resource.
"results": Download a JSON file containing the complete analysis results associated with your supplied token.
"results_gz" Same as "results", but the output will be compress (gzipped).
NULL or Character:
NULL: Save the file to an automatically-generated path.
Character string: A valid file path to save the file to.
(Only when request is "found_ids" or "pathways") Filter results based on the resource. Default is "TOTAL", available choices are:"TOTAL", "UNIPROT", "ENSEMBL", "CHEBI", "IUPHAR", "MIRBASE", "NCBI_PROTEIN", "EMBL", "COMPOUND", "ENTITIES_FDR" or "PUBCHEM_COMPOUND".
rbioapi option(s). See
rba_options's arguments manual for more information on available options.
Token is associated to each Reactome analysis results and kept by Reactome
for at least 7 days. You can locate it in
rba_reactome_analysis's output, under a sub-list named
"summary" (i.e. results$summary$token).
rba_reactome_analysis_pdf to save a full report
in PDF format.
GET https://reactome.org/AnalysisService/download/token/entities/ found/resource/filename.csv" GET https://reactome.org/AnalysisService//download/token/entities/ notfound/filename.csv" GET https://reactome.org/AnalysisService/download/token/pathways/ resource/filename.csv" GET https://reactome.org/AnalysisService/download/token/result.json" GET https://reactome.org/AnalysisService/download/token/result.json.gz"
Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio, The reactome pathway knowledgebase 2022, Nucleic Acids Research, 2021;, kab1028, https://doi.org/10.1093/nar/gkab1028
Griss J, Viteri G, Sidiropoulos K, Nguyen V, Fabregat A, Hermjakob H. ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. Mol Cell Proteomics. 2020 Sep 9. doi: 10.1074/mcp. PubMed PMID: 32907876.