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.

AuthorThomas Sandmann
Date of publicationNone
MaintainerThomas Sandmann <sandmann.t@gmail.com>
LicenseArtistic-2.0
Version1.14.0

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

Functions

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

Files

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

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