gCMAPWeb: A web interface for gene-set enrichment analyses

The gCMAPWeb R package provides a graphical user interface for the gCMAP package. gCMAPWeb uses the Rook package and can be used either on a local machine, leveraging R's internal web server, or run on a dedicated rApache web server installation. gCMAPWeb allows users to search their own data sources and instructions to generate reference datasets from public repositories are included with the package. The package supports three common types of analyses, specifically queries with 1. one or two sets of query gene identifiers, whose members are expected to show changes in gene expression in a consistent direction. For example, an up-regulated gene set might contain genes activated by a transcription factor, a down-regulated geneset targets repressed by the same factor. 2. a single set of query gene identifiers, whose members are expected to show divergent differential expression (non-directional query). For example, members of a particular signaling pathway, some of which may be up- some down-regulated in response to a stimulus. 3. a query with the complete results of a differential expression profiling experiment. For example, gene identifiers and z-scores from a previous perturbation experiment. gCMAPWeb accepts three types of identifiers: EntreIds, gene Symbols and microarray probe ids and can be configured to work with any species supported by Bioconductor. For each query submission, significantly similar reference datasets will be identified and reported in graphical and tabular form.

Author
Thomas Sandmann
Date of publication
None
Maintainer
Thomas Sandmann <sandmann.t@gmail.com>
License
Artistic-2.0
Version
1.14.0

View on Bioconductor

Man pages

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

Files in this package

gCMAPWeb/DESCRIPTION
gCMAPWeb/NAMESPACE
gCMAPWeb/R
gCMAPWeb/R/AllGenerics.R
gCMAPWeb/R/cmap.R
gCMAPWeb/R/cmapAnalysis.R
gCMAPWeb/R/cmapHeatmap.R
gCMAPWeb/R/cmapRun-methods.R
gCMAPWeb/R/createObject.R
gCMAPWeb/R/example_objects.R
gCMAPWeb/R/file_io.R
gCMAPWeb/R/gCMAPWeb-package.R
gCMAPWeb/R/html_elements.R
gCMAPWeb/R/plotting_functions.R
gCMAPWeb/R/reporting.R
gCMAPWeb/build
gCMAPWeb/build/vignette.rds
gCMAPWeb/data
gCMAPWeb/data/cmap1.rdata
gCMAPWeb/data/cmap2.rdata
gCMAPWeb/data/cmap3.rdata
gCMAPWeb/data/cmap4.rdata
gCMAPWeb/data/cmap5.rdata
gCMAPWeb/inst
gCMAPWeb/inst/NEWS.Rd
gCMAPWeb/inst/config
gCMAPWeb/inst/config/config.yml
gCMAPWeb/inst/config/options.txt
gCMAPWeb/inst/config/rapache
gCMAPWeb/inst/config/rapache/gCMAP_app.R
gCMAPWeb/inst/config/rapache/httpd.conf
gCMAPWeb/inst/config/rapache/rapache_config.R
gCMAPWeb/inst/doc
gCMAPWeb/inst/doc/gCMAPWeb.R
gCMAPWeb/inst/doc/gCMAPWeb.Rnw
gCMAPWeb/inst/doc/gCMAPWeb.pdf
gCMAPWeb/inst/doc/referenceDatasets.R
gCMAPWeb/inst/doc/referenceDatasets.Rnw
gCMAPWeb/inst/doc/referenceDatasets.pdf
gCMAPWeb/inst/extdata
gCMAPWeb/inst/extdata/profile_entrez_hs.txt
gCMAPWeb/inst/htdocs
gCMAPWeb/inst/htdocs/brew
gCMAPWeb/inst/htdocs/brew/body_first.html
gCMAPWeb/inst/htdocs/brew/help.md.txt
gCMAPWeb/inst/htdocs/brew/profile_details.html
gCMAPWeb/inst/htdocs/brew/signed_geneset_details.html
gCMAPWeb/inst/htdocs/brew/single_gene_details.html
gCMAPWeb/inst/htdocs/brew/unsigned_geneset_details.html
gCMAPWeb/inst/htdocs/css
gCMAPWeb/inst/htdocs/css/DT_bootstrap.css
gCMAPWeb/inst/htdocs/css/bootstrap-responsive.min.css
gCMAPWeb/inst/htdocs/css/bootstrap.cerulean.min.css
gCMAPWeb/inst/htdocs/css/bootstrap.min.css
gCMAPWeb/inst/htdocs/css/bootstrap.unity.min.css
gCMAPWeb/inst/htdocs/favicon.ico
gCMAPWeb/inst/htdocs/gcmap_analysis.rhtml
gCMAPWeb/inst/htdocs/help.html
gCMAPWeb/inst/htdocs/img
gCMAPWeb/inst/htdocs/img/gene_level_results_pie.png
gCMAPWeb/inst/htdocs/img/gene_level_results_profile.png
gCMAPWeb/inst/htdocs/img/gene_level_results_signed.png
gCMAPWeb/inst/htdocs/img/gene_level_results_unsigned.png
gCMAPWeb/inst/htdocs/img/glyphicons-halflings-white.png
gCMAPWeb/inst/htdocs/img/glyphicons-halflings.png
gCMAPWeb/inst/htdocs/img/index.png
gCMAPWeb/inst/htdocs/img/profile_input.png
gCMAPWeb/inst/htdocs/img/set_level_results.png
gCMAPWeb/inst/htdocs/img/signed_input.png
gCMAPWeb/inst/htdocs/img/sort_asc.png
gCMAPWeb/inst/htdocs/img/sort_asc_disabled.png
gCMAPWeb/inst/htdocs/img/sort_both.png
gCMAPWeb/inst/htdocs/img/sort_desc.png
gCMAPWeb/inst/htdocs/img/sort_desc_disabled.png
gCMAPWeb/inst/htdocs/img/unsigned_input.png
gCMAPWeb/inst/htdocs/index.rhtml
gCMAPWeb/inst/htdocs/input_form_elements.tmp
gCMAPWeb/inst/htdocs/js
gCMAPWeb/inst/htdocs/js/DT_bootstrap.js
gCMAPWeb/inst/htdocs/js/bootstrap.min.js
gCMAPWeb/inst/htdocs/js/gCMAPWeb.js
gCMAPWeb/inst/htdocs/js/jquery-1.8.2.min.js
gCMAPWeb/inst/htdocs/js/jquery.dataTables.min.js
gCMAPWeb/inst/htdocs/js/jquery.dataTables.plugins.js
gCMAPWeb/inst/htdocs/js/jquery.validate.min.js
gCMAPWeb/inst/htdocs/js/underscore-min.js
gCMAPWeb/inst/htdocs/maintenance.html.inactive
gCMAPWeb/inst/htdocs/profile_input.rhtml
gCMAPWeb/inst/htdocs/set_input.rhtml
gCMAPWeb/inst/htdocs/signed_input.rhtml
gCMAPWeb/inst/htdocs/single_input.rhtml
gCMAPWeb/inst/unitTests
gCMAPWeb/inst/unitTests/test_all.R
gCMAPWeb/man
gCMAPWeb/man/addLinks.Rd
gCMAPWeb/man/add_geneScores_to_df.Rd
gCMAPWeb/man/body_first.Rd
gCMAPWeb/man/cmap-data.Rd
gCMAPWeb/man/cmapAnalysis.Rd
gCMAPWeb/man/cmapHeatmap.Rd
gCMAPWeb/man/cmapRun-methods.Rd
gCMAPWeb/man/conversion_html.Rd
gCMAPWeb/man/convert_gene_identifiers.Rd
gCMAPWeb/man/create_GeneIdentifierType.Rd
gCMAPWeb/man/create_GeneSet.Rd
gCMAPWeb/man/create_SignedGeneSet.Rd
gCMAPWeb/man/create_figure_legend.Rd
gCMAPWeb/man/create_gene_report.Rd
gCMAPWeb/man/create_gene_table_legend.Rd
gCMAPWeb/man/create_heatmap_legend.Rd
gCMAPWeb/man/create_legend.Rd
gCMAPWeb/man/create_overview_legend.Rd
gCMAPWeb/man/create_overview_plot.Rd
gCMAPWeb/man/create_profile_ExpressionSet.Rd
gCMAPWeb/man/create_query_objects.Rd
gCMAPWeb/man/create_tab.Rd
gCMAPWeb/man/create_zip.Rd
gCMAPWeb/man/entrez_GeneSets.Rd
gCMAPWeb/man/exampleCMAP.Rd
gCMAPWeb/man/examplePost.Rd
gCMAPWeb/man/gCMAPWeb-package.Rd
gCMAPWeb/man/gCMAPWeb.Rd
gCMAPWeb/man/gene_density_chart_legend.Rd
gCMAPWeb/man/gene_density_profile_legend.Rd
gCMAPWeb/man/gene_pie_chart_legend.Rd
gCMAPWeb/man/generate_report.Rd
gCMAPWeb/man/hide_species_js.Rd
gCMAPWeb/man/html_body_last.Rd
gCMAPWeb/man/html_header.Rd
gCMAPWeb/man/html_table.Rd
gCMAPWeb/man/identifier_radio_html.Rd
gCMAPWeb/man/index_message.Rd
gCMAPWeb/man/index_quote.Rd
gCMAPWeb/man/index_subtitle.Rd
gCMAPWeb/man/index_text.Rd
gCMAPWeb/man/index_title.Rd
gCMAPWeb/man/inputType_buttons.Rd
gCMAPWeb/man/load_cmaps.Rd
gCMAPWeb/man/parse_file_input.Rd
gCMAPWeb/man/parse_request.Rd
gCMAPWeb/man/parse_textarea_input.Rd
gCMAPWeb/man/platform_radio_html.Rd
gCMAPWeb/man/process_score_input.Rd
gCMAPWeb/man/profile_input_example.Rd
gCMAPWeb/man/read_config_file.Rd
gCMAPWeb/man/reference_radio_html.Rd
gCMAPWeb/man/retrieve_annotation.Rd
gCMAPWeb/man/signed_input_example.Rd
gCMAPWeb/man/single_input_example.Rd
gCMAPWeb/man/species_radio_html.Rd
gCMAPWeb/man/stripPrefix.Rd
gCMAPWeb/man/unsigned_input_example.Rd
gCMAPWeb/man/validate_config_file.Rd
gCMAPWeb/man/validate_request.Rd
gCMAPWeb/tests
gCMAPWeb/tests/runTests.R
gCMAPWeb/vignettes
gCMAPWeb/vignettes/esetSlots.png
gCMAPWeb/vignettes/exampleQuery.png
gCMAPWeb/vignettes/gCMAPWeb.Rnw
gCMAPWeb/vignettes/geneLevelPlot.png
gCMAPWeb/vignettes/indexOptions.png
gCMAPWeb/vignettes/referenceDatasets.Rnw
gCMAPWeb/vignettes/setLevelPlot.png
gCMAPWeb/vignettes/tutorial.pdf