Man pages for gCMAPWeb
A web interface for gene-set enrichment analyses

add_geneScores_to_dfCMAPResults data.frame with gene-level scores
addLinksAdding links to columns of a data.frame
body_firstDefinition of html navigation bar elements
cmapAnalysisFunction controlling the gCMAP analysis workflow
cmap-dataExample reference datasets
cmapHeatmapFunction to create an annotated heatmap of gene scores
cmapRun-methodscmapRun
conversion_htmlIdentifier conversion html output
convert_gene_identifiersEntrez mapper
create_figure_legendThis function generates the figure legend, with a separate...
create_GeneIdentifierTypeGeneIdentifierType creator
create_gene_reportThis function compiles a gene-level report from a CMAPResults...
create_GeneSetGeneSet creator
create_gene_table_legendThis function reads an eSet object and returns the html code...
create_heatmap_legendLegend for overview heatmap
create_legendThis function reads a CMAPResults object and returns the html...
create_overview_legendLegend for overview density plot
create_overview_plotOverview plot
create_profile_ExpressionSetExpressionSet creator
create_query_objectsQuery object creator
create_SignedGeneSetSignedGeneSet creator
create_tabCreate tab-delimited output
create_zipExport gCMAPWeb report as zip archive
entrez_GeneSetsGeneSet Entrez mapper
exampleCMAPGenerate example NChannelSets
examplePostSimulate POST request
gCMAPWebStart local gCMAPWeb instance
gCMAPWeb-packageA web-interface for gene-set enrichment analysis
gene_density_chart_legendHtml code for the legend of pie the pie chart of the...
gene_density_profile_legendHtml code for the legend of the density charts of the...
gene_pie_chart_legendHtml code for the legend of the pie chart of the gene-level...
generate_reportgCMAPWeb reporting function
hide_species_jsJavascript code to hide html elements
html_body_lastHtml footer
html_headerHtml header and bootstrap css stylesheet
html_tableFormat data.frame as html table
identifier_radio_htmlHtml code for identifier type radio button selectors
index_messageHtml code for text of the additional message on the index...
index_quoteHtml code for quote on the index page
index_subtitleHtml code for subtitle of the hero unit of the index.rhtml...
index_textHtml code for text of the hero unit of the index.rhtml page
index_titleHtml code for title of the hero unit of the index.rhtml page
inputType_buttonsHtml code for the query type selection buttons on the...
load_cmapsLoading reference datasets
parse_file_inputUploaded file parser
parse_requestPOST request parser
parse_textarea_inputTextarea parser
platform_radio_htmlHtml code for platform radio button selectors
process_score_inputScore parser
profile_input_exampleHtml code for generating an example query button on the...
read_config_fileParser for gCMAPWeb configuration file
reference_radio_htmlHtml code for reference cmap radio button selectors
retrieve_annotationGene symbol and name lookup
signed_input_exampleHtml code for generating and example query button on the...
single_input_exampleHtml code for generating and example query button on the...
species_radio_htmlHtml code for species radio button selectors
stripPrefixStrip prefix from gene identifier names
unsigned_input_exampleHtml code for generating and example query button on the...
validate_config_fileValidation of gCMAPWeb configuration file
validate_requestHtml request validation
gCMAPWeb documentation built on Nov. 17, 2017, 12:30 p.m.