gCMAPWeb-package | A web-interface for gene-set enrichment analysis |
addLinks | Adding links to columns of a data.frame |
add_geneScores_to_df | CMAPResults data.frame with gene-level scores |
body_first | Definition of html navigation bar elements |
cmap-data | Example reference datasets |
cmap1 | Example reference datasets |
cmap2 | Example reference datasets |
cmap3 | Example reference datasets |
cmap4 | Example reference datasets |
cmap5 | Example reference datasets |
cmapAnalysis | Function controlling the gCMAP analysis workflow |
cmapHeatmap | Function to create an annotated heatmap of gene scores |
cmapRun | cmapRun |
cmapRun-method | cmapRun |
conversion_html | Identifier conversion html output |
convert_gene_identifiers | Entrez mapper |
create_figure_legend | This function generates the figure legend, with a separate dom identifier for each output panel |
create_GeneIdentifierType | GeneIdentifierType creator |
create_GeneSet | GeneSet creator |
create_gene_report | This function compiles a gene-level report from a CMAPResults object. |
create_gene_table_legend | This function reads an eSet object and returns the html code to display a legend for all columns that have more descriptive annotations in the varMetadata slot. |
create_heatmap_legend | Legend for overview heatmap |
create_legend | This function reads a CMAPResults object and returns the html code to display a legend for all columns that have more descriptive annotations in the varMetadata slot. A standard set of columns is selected for display in the legend through the 'keep' parameter. In addition, all columns with annotations in the labelDescription field of the varMetadata slot are included if the field content differs from the column name. |
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 |
generate_report | gCMAPWeb reporting function |
gene_density_chart_legend | Html code for the legend of pie the pie chart of the gene-level report |
gene_density_profile_legend | Html code for the legend of the density charts of the gene-level reports from Profile queries |
gene_pie_chart_legend | Html code for the legend of the pie chart of the gene-level report |
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 page (warning box) |
index_quote | Html code for quote on the index page |
index_subtitle | Html code for subtitle of the hero unit of the index.rhtml page |
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 gCMAPWeb index page |
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 profile submission page |
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 signed gene set submission page |
single_input_example | Html code for generating and example query button on the single gene query submission page |
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 unsigned gene set submission page |
validate_config_file | Validation of gCMAPWeb configuration file |
validate_request | Html request validation |