The configurations set for this oncoEnrichR report are outlined below, in addition to an overview of knowledge resources used.
onco_enrich()
html_report_theme
= r onc_enrich_report[['config']][['rmarkdown']][['theme']]
html_floating_toc
= r onc_enrich_report[['config']][['rmarkdown']][['floating_toc']]
query_id_type
= r onc_enrich_report[['config']][['query']][['id_type']]
bgset_id_type
= r onc_enrich_report[['config']][['bgset']][['id_type']]
bgset_description
= r onc_enrich_report[['config']][['enrichment']][['bgset_description']]
Modules included in report:
show_disease
= r onc_enrich_report[['config']][['show']][['disease']]
show_drugs
= r onc_enrich_report[['config']][['show']][['drug']]
show_cancer_hallmarks
= r onc_enrich_report[['config']][['show']][['cancer_hallmark']]
show_fitness
= r onc_enrich_report[['config']][['show']][['fitness']]
show_complex
= r onc_enrich_report[['config']][['show']][['protein_complex']]
show_unknown_function
= r onc_enrich_report[['config']][['show']][['unknown_function']]
show_domain
= r onc_enrich_report[['config']][['show']][['protein_domain']]
show_synleth
= r onc_enrich_report[['config']][['show']][['synleth']]
show_ligand_receptor
= r onc_enrich_report[['config']][['show']][['ligand_receptor']]
show_regulatory
= r onc_enrich_report[['config']][['show']][['regulatory']]
show_subcellcomp
= r onc_enrich_report[['config']][['show']][['subcellcomp']]
show_enrichment
= r onc_enrich_report[['config']][['show']][['enrichment']]
show_cell_tissue
= r onc_enrich_report[['config']][['show']][['cell_tissue']]
show_coexpression
= r onc_enrich_report[['config']][['show']][['coexpression']]
show_aberration
= r onc_enrich_report[['config']][['show']][['aberration']]
show_prognostic
= r onc_enrich_report[['config']][['show']][['cancer_prognosis']]
show_ppi
= r onc_enrich_report[['config']][['show']][['ppi']]
Cancer associations:
show_top_diseases_only
= r onc_enrich_report[['config']][['disease']][['show_top_diseases']]
Regulatory interactions:
regulatory_min_confidence
= r onc_enrich_report[['config']][['regulatory']][['min_confidence']]
Subcellular compartments:
subcellcomp_min_confidence
= r onc_enrich_report[['config']][['subcellcomp']][['minimum_confidence']]
subcellcomp_min_channels
= r onc_enrich_report[['config']][['subcellcomp']][['minimum_channels']]
subcellcomp_show_cytosol
= r onc_enrich_report[['config']][['subcellcomp']][['show_cytosol']]
Gene fitness scores:
fitness_max_score
= r onc_enrich_report[['config']][['fitness']][['max_BF_score']]
Enrichment:
enrichment_p_value_cutoff
= r onc_enrich_report[['config']][['enrichment']][['p_value_cutoff']]
enrichment_q_value_cutoff
= r onc_enrich_report[['config']][['enrichment']][['q_value_cutoff']]
enrichment_p_value_adj
= r onc_enrich_report[['config']][['enrichment']][['p_adjust_method']]
enrichment_min_geneset_size
= r onc_enrich_report[['config']][['enrichment']][['min_gs_size']]
enrichment_max_geneset_size
= r onc_enrich_report[['config']][['enrichment']][['max_gs_size']]
enrichment_simplify_go
= r onc_enrich_report[['config']][['enrichment']][['simplify_go']]
enrichment_plot_num_terms
= r onc_enrich_report[['config']][['enrichment']][['enrichment_plot_num_terms']]
Protein-protein interactions:
ppi_string_min_score
= r onc_enrich_report[['config']][['ppi']][['string']][['minimum_score']]
ppi_string_network_type
= r onc_enrich_report[['config']][['ppi']][['string']][['network_type']]
ppi_biogrid_min_evidence
= r onc_enrich_report[['config']][['ppi']][['biogrid']][['minimum_evidence']]
ppi_add_nodes
= r onc_enrich_report[['config']][['ppi']][['string']][['add_nodes']]
ppi_node_shadow
= r onc_enrich_report[['config']][['ppi']][['string']][['visnetwork_shadow']]
ppi_show_drugs
= r onc_enrich_report[['config']][['ppi']][['string']][['show_drugs']]
ppi_show_isolated_nodes
= r onc_enrich_report[['config']][['ppi']][['string']][['show_isolated_nodes']]
The analysis performed in the oncoEnrichR report is based on the following main tools and knowledge resources:
for(n in names(onc_enrich_report[['config']][['resources']])){ if(onc_enrich_report[['config']][['resources']][[n]]$resource_type == 'software'){ license <- onc_enrich_report[['config']][['resources']][[n]]$license s <- glue::glue( " * [{onc_enrich_report[['config']][['resources']][[n]]$name}]", "({onc_enrich_report[['config']][['resources']][[n]]$url}) - ", "{onc_enrich_report[['config']][['resources']][[n]]$description} ", "({onc_enrich_report[['config']][['resources']][[n]]$version}) - ", "[{onc_enrich_report[['config']][['resources']][[n]]$license}]", "({onc_enrich_report[['config']][['resources']][[n]]$license_url})") if(license == "."){ s <- glue::glue( " * [{onc_enrich_report[['config']][['resources']][[n]]$name}]", "({onc_enrich_report[['config']][['resources']][[n]]$url}) - ", "{onc_enrich_report[['config']][['resources']][[n]]$description} ", "({onc_enrich_report[['config']][['resources']][[n]]$version}) - ", "**See below for licensing requirements**") }else if(license == "Open Access"){ s <- glue::glue( " * [{onc_enrich_report[['config']][['resources']][[n]]$name}]", "({onc_enrich_report[['config']][['resources']][[n]]$url}) - ", "{onc_enrich_report[['config']][['resources']][[n]]$description} ", "({onc_enrich_report[['config']][['resources']][[n]]$version}) - ", "*Open Access*") } cat(s,sep="\n") } }
for(n in names(onc_enrich_report[['config']][['resources']])){ if(onc_enrich_report[['config']][['resources']][[n]]$resource_type != 'software'){ license <- onc_enrich_report[['config']][['resources']][[n]]$license s <- glue::glue( " * [{onc_enrich_report[['config']][['resources']][[n]]$name}]", "({onc_enrich_report[['config']][['resources']][[n]]$url}) - ", "{onc_enrich_report[['config']][['resources']][[n]]$description} ", "({onc_enrich_report[['config']][['resources']][[n]]$version}) - ", "[{onc_enrich_report[['config']][['resources']][[n]]$license}]", "({onc_enrich_report[['config']][['resources']][[n]]$license_url})") if(license == "."){ s <- glue::glue( " * [{onc_enrich_report[['config']][['resources']][[n]]$name}]", "({onc_enrich_report[['config']][['resources']][[n]]$url}) - ", "{onc_enrich_report[['config']][['resources']][[n]]$description} ", "({onc_enrich_report[['config']][['resources']][[n]]$version}) - ", "**<sup>\\*</sup>See below for licensing requirements**") }else if(license == "Open Access"){ s <- glue::glue( " * [{onc_enrich_report[['config']][['resources']][[n]]$name}]", "({onc_enrich_report[['config']][['resources']][[n]]$url}) - ", "{onc_enrich_report[['config']][['resources']][[n]]$description} ", "({onc_enrich_report[['config']][['resources']][[n]]$version}) - ", "*Open Access*") } cat(s,sep="\n") } } cat(glue::glue( " <br><br><sup>\\*</sup>*[KEGG]({onc_enrich_report[['config']][['resources']][['kegg']]$url})", " and [CGC]({onc_enrich_report[['config']][['resources']][['cgc']]$url}) are freely", " available for academic, non-commercial", " use. For commercial usage, end users need to consult [https://www.pathway.jp](https://www.pathway.jp/)", " and [https://cancer.sanger.ac.uk/cosmic/license](https://cancer.sanger.ac.uk/cosmic/license)", " for licensing inquiries.*<br><br>"), sep="\n")
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