gCMAPWeb: A web interface for gene-set enrichment analyses
Version 1.16.0

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.

AuthorThomas Sandmann
Bioconductor views DifferentialExpression GUI GeneExpression GeneSetEnrichment Microarray Transcription Visualization
Date of publicationNone
MaintainerThomas Sandmann <sandmann.t@gmail.com>
LicenseArtistic-2.0
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("gCMAPWeb")

Getting started

Package overview

Popular man pages

create_overview_plot: Overview plot
create_profile_ExpressionSet: ExpressionSet creator
exampleCMAP: Generate example NChannelSets
gCMAPWeb-package: A web-interface for gene-set enrichment analysis
gene_density_profile_legend: Html code for the legend of the density charts of the...
index_subtitle: Html code for subtitle of the hero unit of the index.rhtml...
validate_config_file: Validation of gCMAPWeb configuration file
See all...

All man pages Function index File listing

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

Functions

ImagePlot Source code
addLinks Man page Source code
add_geneScores_to_df Man page Source code
alias2entrez Source code
body_first Man page Source code
cmap-data Man page
cmap1 Man page
cmap2 Man page
cmap3 Man page
cmap4 Man page
cmap5 Man page
cmapAnalysis Man page Source code
cmapHeatmap Man page Source code
cmapRun Man page
cmapRun,CMAPCollection,CMAPCollection-method Man page
cmapRun,CMAPCollection,eSet-method Man page
cmapRun,GeneSet,CMAPCollection-method Man page
cmapRun,GeneSet,eSet-method Man page
cmapRun,SignedGeneSet,eSet-method Man page
cmapRun,eSet,CMAPCollection-method Man page
cmapRun,eSet,eSet-method Man page
conversion_html Man page Source code
convert_gene_identifiers Man page Source code
create_GeneIdentifierType Man page Source code
create_GeneSet Man page Source code
create_SignedGeneSet Man page Source code
create_figure_legend Man page Source code
create_gene_report Man page Source code
create_gene_table_legend Man page Source code
create_heatmap_legend Man page Source code
create_legend Man page Source code
create_overview_legend Man page Source code
create_overview_plot Man page Source code
create_profile_ExpressionSet Man page Source code
create_query_objects Man page Source code
create_tab Man page Source code
create_zip Man page Source code
entrez2symbol Source code
entrez_GeneSets Man page Source code
exampleCMAP Man page Source code
examplePost Man page Source code
gCMAPWeb Man page Source code
gCMAPWeb-package Man page
gene.set.density Source code
gene_density_chart_legend Man page Source code
gene_density_profile_legend Man page Source code
gene_pie_chart_legend Man page Source code
gene_score_density Source code
gene_set.pie Source code
generate_report Man page Source code
hide_species_js Man page Source code
html_body_last Man page Source code
html_header Man page Source code
html_table Man page Source code
identifier_radio_html Man page Source code
index_message Man page Source code
index_quote Man page Source code
index_subtitle Man page Source code
index_text Man page Source code
index_title Man page Source code
inputType_buttons Man page Source code
load_cmaps Man page Source code
overview.density Source code
overview.heatmap Source code
parse_file_input Man page Source code
parse_request Man page Source code
parse_textarea_input Man page Source code
platform_radio_html Man page Source code
probe2entrez Source code
process_score_input Man page Source code
profile_input_example Man page Source code
read_config_file Man page Source code
reference_radio_html Man page Source code
retrieve_annotation Man page Source code
signed_input_example Man page Source code
single_input_example Man page Source code
species_radio_html Man page Source code
stripPrefix Man page Source code
unsigned_input_example Man page Source code
validate_config_file Man page Source code
validate_request Man page Source code

Files

.BBSoptions
DESCRIPTION
NAMESPACE
R
R/AllGenerics.R
R/cmap.R
R/cmapAnalysis.R
R/cmapHeatmap.R
R/cmapRun-methods.R
R/createObject.R
R/example_objects.R
R/file_io.R
R/gCMAPWeb-package.R
R/html_elements.R
R/plotting_functions.R
R/reporting.R
build
build/vignette.rds
data
data/cmap1.rdata
data/cmap2.rdata
data/cmap3.rdata
data/cmap4.rdata
data/cmap5.rdata
inst
inst/CITATION
inst/NEWS.Rd
inst/config
inst/config/config.yml
inst/config/options.txt
inst/config/rapache
inst/config/rapache/gCMAP_app.R
inst/config/rapache/httpd.conf
inst/config/rapache/rapache_config.R
inst/doc
inst/doc/gCMAPWeb.R
inst/doc/gCMAPWeb.Rnw
inst/doc/gCMAPWeb.pdf
inst/doc/referenceDatasets.R
inst/doc/referenceDatasets.Rnw
inst/doc/referenceDatasets.pdf
inst/extdata
inst/extdata/profile_entrez_hs.txt
inst/htdocs
inst/htdocs/brew
inst/htdocs/brew/body_first.html
inst/htdocs/brew/help.md.txt
inst/htdocs/brew/profile_details.html
inst/htdocs/brew/signed_geneset_details.html
inst/htdocs/brew/single_gene_details.html
inst/htdocs/brew/unsigned_geneset_details.html
inst/htdocs/css
inst/htdocs/css/DT_bootstrap.css
inst/htdocs/css/bootstrap-responsive.min.css
inst/htdocs/css/bootstrap.cerulean.min.css
inst/htdocs/css/bootstrap.min.css
inst/htdocs/css/bootstrap.unity.min.css
inst/htdocs/favicon.ico
inst/htdocs/gcmap_analysis.rhtml
inst/htdocs/help.html
inst/htdocs/img
inst/htdocs/img/gene_level_results_pie.png
inst/htdocs/img/gene_level_results_profile.png
inst/htdocs/img/gene_level_results_signed.png
inst/htdocs/img/gene_level_results_unsigned.png
inst/htdocs/img/glyphicons-halflings-white.png
inst/htdocs/img/glyphicons-halflings.png
inst/htdocs/img/index.png
inst/htdocs/img/profile_input.png
inst/htdocs/img/set_level_results.png
inst/htdocs/img/signed_input.png
inst/htdocs/img/sort_asc.png
inst/htdocs/img/sort_asc_disabled.png
inst/htdocs/img/sort_both.png
inst/htdocs/img/sort_desc.png
inst/htdocs/img/sort_desc_disabled.png
inst/htdocs/img/unsigned_input.png
inst/htdocs/index.rhtml
inst/htdocs/input_form_elements.tmp
inst/htdocs/js
inst/htdocs/js/DT_bootstrap.js
inst/htdocs/js/bootstrap.min.js
inst/htdocs/js/gCMAPWeb.js
inst/htdocs/js/jquery-1.8.2.min.js
inst/htdocs/js/jquery.dataTables.min.js
inst/htdocs/js/jquery.dataTables.plugins.js
inst/htdocs/js/jquery.validate.min.js
inst/htdocs/js/underscore-min.js
inst/htdocs/maintenance.html.inactive
inst/htdocs/profile_input.rhtml
inst/htdocs/set_input.rhtml
inst/htdocs/signed_input.rhtml
inst/htdocs/single_input.rhtml
inst/unitTests
inst/unitTests/test_all.R
man
man/addLinks.Rd
man/add_geneScores_to_df.Rd
man/body_first.Rd
man/cmap-data.Rd
man/cmapAnalysis.Rd
man/cmapHeatmap.Rd
man/cmapRun-methods.Rd
man/conversion_html.Rd
man/convert_gene_identifiers.Rd
man/create_GeneIdentifierType.Rd
man/create_GeneSet.Rd
man/create_SignedGeneSet.Rd
man/create_figure_legend.Rd
man/create_gene_report.Rd
man/create_gene_table_legend.Rd
man/create_heatmap_legend.Rd
man/create_legend.Rd
man/create_overview_legend.Rd
man/create_overview_plot.Rd
man/create_profile_ExpressionSet.Rd
man/create_query_objects.Rd
man/create_tab.Rd
man/create_zip.Rd
man/entrez_GeneSets.Rd
man/exampleCMAP.Rd
man/examplePost.Rd
man/gCMAPWeb-package.Rd
man/gCMAPWeb.Rd
man/gene_density_chart_legend.Rd
man/gene_density_profile_legend.Rd
man/gene_pie_chart_legend.Rd
man/generate_report.Rd
man/hide_species_js.Rd
man/html_body_last.Rd
man/html_header.Rd
man/html_table.Rd
man/identifier_radio_html.Rd
man/index_message.Rd
man/index_quote.Rd
man/index_subtitle.Rd
man/index_text.Rd
man/index_title.Rd
man/inputType_buttons.Rd
man/load_cmaps.Rd
man/parse_file_input.Rd
man/parse_request.Rd
man/parse_textarea_input.Rd
man/platform_radio_html.Rd
man/process_score_input.Rd
man/profile_input_example.Rd
man/read_config_file.Rd
man/reference_radio_html.Rd
man/retrieve_annotation.Rd
man/signed_input_example.Rd
man/single_input_example.Rd
man/species_radio_html.Rd
man/stripPrefix.Rd
man/unsigned_input_example.Rd
man/validate_config_file.Rd
man/validate_request.Rd
tests
tests/runTests.R
vignettes
vignettes/esetSlots.png
vignettes/exampleQuery.png
vignettes/gCMAPWeb.Rnw
vignettes/geneLevelPlot.png
vignettes/indexOptions.png
vignettes/referenceDatasets.Rnw
vignettes/setLevelPlot.png
vignettes/tutorial.pdf
gCMAPWeb documentation built on May 20, 2017, 9:42 p.m.

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