Man pages for gCMAPWeb
A web interface for gene-set enrichment analyses
| add_geneScores_to_df | CMAPResults data.frame with gene-level scores |
| addLinks | Adding links to columns of a data.frame |
| body_first | Definition of html navigation bar elements |
| cmapAnalysis | Function controlling the gCMAP analysis workflow |
| cmap-data | Example reference datasets |
| cmapHeatmap | Function to create an annotated heatmap of gene scores |
| cmapRun-methods | cmapRun |
| conversion_html | Identifier conversion html output |
| convert_gene_identifiers | Entrez mapper |
| create_figure_legend | This function generates the figure legend, with a separate... |
| create_GeneIdentifierType | GeneIdentifierType creator |
| create_gene_report | This function compiles a gene-level report from a CMAPResults... |
| create_GeneSet | GeneSet creator |
| create_gene_table_legend | This function reads an eSet object and returns the html code... |
| create_heatmap_legend | Legend for overview heatmap |
| create_legend | This function reads a CMAPResults object and returns the html... |
| create_overview_legend | Legend for overview density plot |
| create_overview_plot | Overview plot |
| create_profile_ExpressionSet | ExpressionSet creator |
| create_query_objects | Query object creator |
| create_SignedGeneSet | SignedGeneSet creator |
| create_tab | Create tab-delimited output |
| create_zip | Export gCMAPWeb report as zip archive |
| entrez_GeneSets | GeneSet Entrez mapper |
| exampleCMAP | Generate example NChannelSets |
| examplePost | Simulate POST request |
| gCMAPWeb | Start local gCMAPWeb instance |
| gCMAPWeb-package | A web-interface for gene-set enrichment analysis |
| gene_density_chart_legend | Html code for the legend of pie the pie chart of the... |
| gene_density_profile_legend | Html code for the legend of the density charts of the... |
| gene_pie_chart_legend | Html code for the legend of the pie chart of the gene-level... |
| generate_report | gCMAPWeb reporting function |
| hide_species_js | Javascript code to hide html elements |
| html_body_last | Html footer |
| html_header | Html header and bootstrap css stylesheet |
| html_table | Format data.frame as html table |
| identifier_radio_html | Html code for identifier type radio button selectors |
| index_message | Html code for text of the additional message on the index... |
| index_quote | Html code for quote on the index page |
| index_subtitle | Html code for subtitle of the hero unit of the index.rhtml... |
| index_text | Html code for text of the hero unit of the index.rhtml page |
| index_title | Html code for title of the hero unit of the index.rhtml page |
| inputType_buttons | Html code for the query type selection buttons on the... |
| load_cmaps | Loading reference datasets |
| parse_file_input | Uploaded file parser |
| parse_request | POST request parser |
| parse_textarea_input | Textarea parser |
| platform_radio_html | Html code for platform radio button selectors |
| process_score_input | Score parser |
| profile_input_example | Html code for generating an example query button on the... |
| read_config_file | Parser for gCMAPWeb configuration file |
| reference_radio_html | Html code for reference cmap radio button selectors |
| retrieve_annotation | Gene symbol and name lookup |
| signed_input_example | Html code for generating and example query button on the... |
| single_input_example | Html code for generating and example query button on the... |
| species_radio_html | Html code for species radio button selectors |
| stripPrefix | Strip prefix from gene identifier names |
| unsigned_input_example | Html code for generating and example query button on the... |
| validate_config_file | Validation of gCMAPWeb configuration file |
| validate_request | Html request validation |
