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
cmapAnalysis            Function controlling the gCMAP analysis
                        workflow
cmapHeatmap             Function to create an annotated heatmap of gene
                        scores
cmapRun                 cmapRun
conversion_html         Identifier conversion html output
convert_gene_identifiers
                        Entrez mapper
create_GeneIdentifierType
                        GeneIdentifierType creator
create_GeneSet          GeneSet creator
create_SignedGeneSet    SignedGeneSet creator
create_figure_legend    This function generates the figure legend, with
                        a separate dom identifier for each output panel
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_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-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
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 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
trim                    Function to trim leading / tailing whitespace
                        characters
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
