bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis
Version 1.4.0

bioCancer is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.

Browse man pages Browse package API and functions Browse package files

AuthorKarim Mezhoud [aut, cre]
Bioconductor views DataRepresentation GUI GeneExpression GeneTarget MultipleComparison Network Pathways Reactome Visualization
Date of publicationNone
MaintainerKarim Mezhoud <kmezhoud@gmail.com>
LicenseAGPL-3 | file LICENSE
Version1.4.0
URL http://kmezhoud.github.io/bioCancer
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("bioCancer")

Man pages

attriColorGene: Attribute Color to Gene
attriColorValue: Attribute Color to Value
attriColorVector: Attribute color to a vector of numeric values
attriShape2Gene: Attribute shape to nodes
attriShape2Node: Attributes shape to Nodes
bioCancer: Launch bioCancer with default browser
checkDimensions: Chech wich Cases and genetic profiles are available for every...
coffeewheel: This is an htmlwidgets-based visualization tool for...
coffeewheelOutput: Widget output function for use in Shiny
displayTable: Display dataframe in table using DT package
Edges_Diseases_obj: get Edges dataframe for Gene/Disease association from...
getFreqMutData: get mutation frequency
getGenesClassification: get genes classification
getList_Cases: get list of cases of each selected study in Classifier panel
getList_GenProfs: get list of genetic profiles of each selected study in...
getListProfData: get list of data frame with profiles data (CNA,mRNA,...
getMegaProfData: search and get genetic profiles (CNA,mRNA, Methylation,...
grepRef: search and get genetic profiles (CNA,mRNA, Methylation,...
metabologram: Circular plot of hierarchital data of genetic profile.
Mutation_obj: Atribute mutation frequency to nodes
Node_df_FreqIn: Attributes size to Nodes depending on number of interaction
Node_Diseases_obj: Attributes color and shape to Nodes of Diseases
Node_obj_CNA_ProfData: Attribute CNA data to node border
Node_obj_FreqIn: Attribute interaction frequency to node size
Node_obj_Met_ProfData: Attribute gene Methylation to Nodes
Node_obj_mRNA_Classifier: Atrribute genes expression to color nodes
renderCoffeewheel: Widget render function for use in Shiny
reStrColorGene: Restructure the list of color attributed to the genes in...
reStrDimension: Restructure the list of color attributed to the genes in...
reStrDisease: Restructure the list of color attributed to the genes in...
sampleWheelData: Sample data for wheel initialization
Studies_obj: get object for grViz. Link Studies to genes
UnifyRowNames: Unify row names in data frame with the same order of gene...
whichGeneList: Verify which gene list is selected

Functions

Edges_Diseases_obj Man page Source code
Mutation_obj Man page Source code
Node_Diseases_obj Man page Source code
Node_df_FreqIn Man page Source code
Node_obj_CNA_ProfData Man page Source code
Node_obj_FreqIn Man page Source code
Node_obj_Met_ProfData Man page Source code
Node_obj_mRNA_Classifier Man page Source code
Studies_obj Man page Source code
UnifyRowNames Man page Source code
attriColorGene Man page Source code
attriColorValue Man page Source code
attriColorVector Man page Source code
attriShape2Gene Man page Source code
attriShape2Node Man page Source code
bioCancer Man page Source code
bioCancer-package Man page
checkDimensions Man page Source code
coffeewheel Man page Source code
coffeewheelOutput Man page Source code
displayTable Man page Source code
getFreqMutData Man page Source code
getGenesClassification Man page Source code
getListProfData Man page Source code
getList_Cases Man page Source code
getList_GenProfs Man page Source code
getMegaProfData Man page Source code
grepRef Man page Source code
metabologram Man page Source code
onLoad Source code
reStrColorGene Man page Source code
reStrDimension Man page Source code
reStrDisease Man page Source code
renderCoffeewheel Man page Source code
sampleWheelData Man page
whichGeneList Man page Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/Enrich.R
R/Portal.R
R/Reactome.R
R/aaa.R
R/bioCancer.R
R/coffeewheel.R
R/dyNetwork.R
R/geNetClassifier.R
R/getListProfData.R
R/getMegaProfData.R
R/metabologram.R
R/zzz.R
README.md
bioCancer.Rproj
build
build/vignette.rds
inst
inst/Rbis
inst/Rbis/cbindna.R
inst/Rbis/combine.R
inst/Rbis/compare_means.R
inst/Rbis/compare_props.R
inst/Rbis/conjoint.R
inst/Rbis/conjoint_profiles.R
inst/Rbis/correlation.R
inst/Rbis/cross_tabs.R
inst/Rbis/dtree.R
inst/Rbis/explore.R
inst/Rbis/full_factor.R
inst/Rbis/glm_reg.R
inst/Rbis/goodness.R
inst/Rbis/hier_clus.R
inst/Rbis/kmeans_clus.R
inst/Rbis/mds.R
inst/Rbis/performance.R
inst/Rbis/pivotr.R
inst/Rbis/pmap.R
inst/Rbis/pre_factor.R
inst/Rbis/prob_calc.R
inst/Rbis/radiant.R
inst/Rbis/rbindna.R
inst/Rbis/regression.R
inst/Rbis/rfm.R
inst/Rbis/sample_size.R
inst/Rbis/sampling.R
inst/Rbis/simulater.R
inst/Rbis/single_mean.R
inst/Rbis/single_prop.R
inst/Rbis/transform.R
inst/Rbis/visualize.R
inst/base
inst/base/bioCancerInit.R
inst/base/data
inst/base/data/GeneList
inst/base/data/GeneList/102.txt
inst/base/data/GeneList/1021.txt
inst/base/data/GeneList/223.txt
inst/base/data/GeneList/555.txt
inst/base/data/GeneList/73.txt
inst/base/data/GeneList/DNA_damage_Response.txt
inst/base/data/GeneList/Glioblastoma_RTK_Ras_PI3K_AKT_Signaling.txt
inst/base/data/GeneList/INvasion_and_Metastasis.txt
inst/base/data/GeneList/ProstateCancer_AR_and_Steroid_synthesis_enzymes.txt
inst/base/data/GeneList/ProstateCancer_DownRegulated_by_Androgen.txt
inst/base/data/epiGenomics.rda
inst/base/global.R
inst/base/init.R
inst/base/server_bkp.R
inst/base/tools
inst/base/tools/app
inst/base/tools/app/about.md
inst/base/tools/app/code.R
inst/base/tools/app/help.R
inst/base/tools/app/report.R
inst/base/tools/app/state.R
inst/base/tools/app/stop.R
inst/base/tools/app/tutorials.md
inst/base/tools/data
inst/base/tools/data/Circomics_ui.R
inst/base/tools/data/Classifier.R
inst/base/tools/data/Classifier_ui.R
inst/base/tools/data/ClinicalData.R
inst/base/tools/data/ClinicalData_ui.R
inst/base/tools/data/DisGeNet.R
inst/base/tools/data/MutData.R
inst/base/tools/data/MutData_ui.R
inst/base/tools/data/Network.R
inst/base/tools/data/Network3D.R
inst/base/tools/data/NetworkD3_ui.R
inst/base/tools/data/Network_ui.R
inst/base/tools/data/ProfData.R
inst/base/tools/data/ProfData_ui.R
inst/base/tools/data/Reactome.R
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inst/base/tools/data/getCircomics.R
inst/base/tools/data/getReactomeFUN.R
inst/base/tools/data/manage.R
inst/base/tools/data/manage_ui.R
inst/base/tools/data/pivotr_ui.R
inst/base/tools/data/transform_ui.R
inst/base/tools/data/ui_data.R
inst/base/tools/data/view.R
inst/base/tools/data/visualize_ui.R
inst/base/tools/help
inst/base/tools/help/Circomics.md
inst/base/tools/help/Classifier.md
inst/base/tools/help/Clinical.md
inst/base/tools/help/Mutation.md
inst/base/tools/help/Profiles.md
inst/base/tools/help/Reactome.md
inst/base/tools/help/Studies.md
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inst/base/tools/help/combine.Rmd
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inst/base/tools/help/figures/Plot_enrich.png
inst/base/tools/help/figures/ReactomeLegend.png
inst/base/tools/help/figures/Reactome_Network.png
inst/base/tools/help/figures/anti_join.png
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inst/base/tools/help/figures/combine_avengers_superheroes.png
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inst/base/tools/help/figures/explore.png
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inst/base/tools/help/figures/overview_methods.png
inst/base/tools/help/figures/pivotr.png
inst/base/tools/help/figures/right_join.png
inst/base/tools/help/manage.md
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inst/base/tools/help/report.md
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inst/base/tools/help/transform.Rmd
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inst/base/ui_bkp.R
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inst/base/www/rmarkdown/dagre-0.4.0
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inst/bioCancer
inst/bioCancer/bioCancerInit.R
inst/bioCancer/data
inst/bioCancer/data/GeneList
inst/bioCancer/data/user_CNA.rda
inst/bioCancer/data/user_MetHM27.rda
inst/bioCancer/data/user_MetHM450.rda
inst/bioCancer/data/user_Mut.rda
inst/bioCancer/data/user_mRNA.rda
inst/bioCancer/global.R
inst/bioCancer/rsconnect
inst/bioCancer/rsconnect/shinyapps.io
inst/bioCancer/rsconnect/shinyapps.io/kmezhoud
inst/bioCancer/rsconnect/shinyapps.io/kmezhoud/bioCancer.dcf
inst/bioCancer/server.R
inst/bioCancer/tools
inst/bioCancer/tools/analysis
inst/bioCancer/tools/analysis/conjoint_profiles_ui.R
inst/bioCancer/tools/analysis/conjoint_ui.R
inst/bioCancer/tools/analysis/full_factor_ui.R
inst/bioCancer/tools/analysis/hier_clus_ui.R
inst/bioCancer/tools/analysis/kmeans_clus_ui.R
inst/bioCancer/tools/analysis/mds_ui.R
inst/bioCancer/tools/analysis/pmap_ui.R
inst/bioCancer/tools/analysis/pre_factor_ui.R
inst/bioCancer/tools/help
inst/bioCancer/tools/help/conjoint.md
inst/bioCancer/tools/help/conjoint_profiles.md
inst/bioCancer/tools/help/figures
inst/bioCancer/tools/help/figures/conjoint_carpet_design.png
inst/bioCancer/tools/help/figures/conjoint_corr_mat.png
inst/bioCancer/tools/help/figures/conjoint_plot.png
inst/bioCancer/tools/help/figures/conjoint_profiles.png
inst/bioCancer/tools/help/figures/conjoint_summary.png
inst/bioCancer/tools/help/figures/full_factor_plot.png
inst/bioCancer/tools/help/figures/full_factor_plot_rotation.png
inst/bioCancer/tools/help/figures/full_factor_summary.png
inst/bioCancer/tools/help/figures/full_factor_summary_shopping.png
inst/bioCancer/tools/help/figures/hier_clus_dendro.png
inst/bioCancer/tools/help/figures/hier_clus_scree.png
inst/bioCancer/tools/help/figures/kmeans_clus_cross_tabs_plot.png
inst/bioCancer/tools/help/figures/kmeans_clus_cross_tabs_summary.png
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inst/bioCancer/tools/help/figures/mds_plot.png
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inst/bioCancer/tools/help/figures/mds_plot_tpbrands.png
inst/bioCancer/tools/help/figures/mds_summary.png
inst/bioCancer/tools/help/figures/mds_summary_tpbrands.png
inst/bioCancer/tools/help/figures/pmap_plot_all.png
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inst/bioCancer/tools/help/figures/pmap_plot_brands_attr.png
inst/bioCancer/tools/help/figures/pmap_summary.png
inst/bioCancer/tools/help/figures/pre_factor_summary_plot.png
inst/bioCancer/tools/help/full_factor.md
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inst/bioCancer/tools/help/mds.md
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inst/doc
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inst/doc/rmd2pdf.R
inst/extdata
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inst/quant/tools/help/figures/regression_log_diamonds_scatter.png
inst/quant/tools/help/figures/regression_log_diamonds_summary.png
inst/quant/tools/help/figures/regression_log_diamonds_viz_scatter.png
inst/quant/tools/help/figures/regression_predict.png
inst/quant/tools/help/figures/regression_summary.png
inst/quant/tools/help/figures/sample_size_ex1a.png
inst/quant/tools/help/figures/sample_size_ex1b.png
inst/quant/tools/help/figures/sample_size_ex2a.png
inst/quant/tools/help/figures/sample_size_ex2b.png
inst/quant/tools/help/figures/sampling.png
inst/quant/tools/help/figures/simulater.png
inst/quant/tools/help/figures/simulater_repeat.png
inst/quant/tools/help/figures/simulater_view.png
inst/quant/tools/help/figures/simulater_viz.png
inst/quant/tools/help/figures/single_mean_plot.png
inst/quant/tools/help/figures/single_mean_prob_calc.png
inst/quant/tools/help/figures/single_mean_summary.png
inst/quant/tools/help/figures/single_prop_prob_calc_p.png
inst/quant/tools/help/figures/single_prop_prob_calc_v.png
inst/quant/tools/help/figures/single_prop_summary.png
inst/quant/tools/help/figures/single_proportion_prob_calc_p.png
inst/quant/tools/help/figures/single_proportion_prob_calc_v.png
inst/quant/tools/help/figures/single_proportion_summary.png
inst/quant/tools/help/glm_reg.Rmd
inst/quant/tools/help/glm_reg.md
inst/quant/tools/help/prob_calc.Rmd
inst/quant/tools/help/prob_calc.md
inst/quant/tools/help/regression.Rmd
inst/quant/tools/help/regression.md
inst/quant/tools/help/sample_size.Rmd
inst/quant/tools/help/sample_size.md
inst/quant/tools/help/sampling.md
inst/quant/tools/help/simulater.Rmd
inst/quant/tools/help/simulater.md
inst/quant/tools/help/single_mean.md
inst/quant/tools/help/single_prop.Rmd
inst/quant/tools/help/single_prop.md
inst/rsconnect
inst/rsconnect/shinyapps.io
inst/rsconnect/shinyapps.io/kmezhoud
inst/rsconnect/shinyapps.io/kmezhoud/inst.dcf
man
man/Edges_Diseases_obj.Rd
man/Mutation_obj.Rd
man/Node_Diseases_obj.Rd
man/Node_df_FreqIn.Rd
man/Node_obj_CNA_ProfData.Rd
man/Node_obj_FreqIn.Rd
man/Node_obj_Met_ProfData.Rd
man/Node_obj_mRNA_Classifier.Rd
man/Studies_obj.Rd
man/UnifyRowNames.Rd
man/attriColorGene.Rd
man/attriColorValue.Rd
man/attriColorVector.Rd
man/attriShape2Gene.Rd
man/attriShape2Node.Rd
man/bioCancer.Rd
man/checkDimensions.Rd
man/coffeewheel.Rd
man/coffeewheelOutput.Rd
man/displayTable.Rd
man/getFreqMutData.Rd
man/getGenesClassification.Rd
man/getListProfData.Rd
man/getList_Cases.Rd
man/getList_GenProfs.Rd
man/getMegaProfData.Rd
man/grepRef.Rd
man/metabologram.Rd
man/reStrColorGene.Rd
man/reStrDimension.Rd
man/reStrDisease.Rd
man/renderCoffeewheel.Rd
man/sampleWheelData.Rd
man/whichGeneList.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_funs.R
vignettes
vignettes/bioCancer.Rmd
vignettes/figures
vignettes/figures/80x15.png
vignettes/figures/Classifier_Table.png
vignettes/figures/Plot_enrich.png
vignettes/figures/ReactomeLegend.png
vignettes/figures/Reactome_Network.png
vignettes/figures/anti_join.png
vignettes/figures/boxplot.png
vignettes/figures/combine_avengers_superheroes.png
vignettes/figures/compareClusterDO.png
vignettes/figures/compareClusterGO.png
vignettes/figures/compareClusterKEGG.png
vignettes/figures/explore.png
vignettes/figures/full_join.png
vignettes/figures/inner_join.png
vignettes/figures/join_publishers_superheroes.png
vignettes/figures/join_superheroes_publishers.png
vignettes/figures/left_join.png
vignettes/figures/merge_heroes_publishers.png
vignettes/figures/merge_publishers_heroes.png
vignettes/figures/outer_join.png
vignettes/figures/overview_methods.png
vignettes/figures/pivotr.png
vignettes/figures/right_join.png
bioCancer documentation built on May 20, 2017, 10:54 p.m.