Package: bioCancer 1.33.0

Karim Mezhoud

bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis

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

Authors:Karim Mezhoud [aut, cre]

bioCancer_1.33.0.tar.gz
bioCancer_1.33.0.zip(r-4.5)bioCancer_1.33.0.zip(r-4.4)bioCancer_1.33.0.zip(r-4.3)
bioCancer_1.33.0.tgz(r-4.4-any)bioCancer_1.33.0.tgz(r-4.3-any)
bioCancer_1.33.0.tar.gz(r-4.5-noble)bioCancer_1.33.0.tar.gz(r-4.4-noble)
bioCancer_1.33.0.tgz(r-4.4-emscripten)bioCancer_1.33.0.tgz(r-4.3-emscripten)
bioCancer.pdf |bioCancer.html✨
bioCancer/json (API)
NEWS

# Install 'bioCancer' in R:
install.packages('bioCancer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/kmezhoud/biocancer/issues

Datasets:

On BioConductor:bioCancer-1.33.0(bioc 3.20)bioCancer-1.32.0(bioc 3.19)

guidatarepresentationnetworkmultiplecomparisonpathwaysreactomevisualizationgeneexpressiongenetargetanalysisbiocancer-interfacecancercancer-studiesrmarkdown

46 exports 20 stars 6.32 score 246 dependencies 7 scripts 197 downloads

Last updated 5 months agofrom:a8895588ab. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 21 2024
R-4.5-winNOTESep 21 2024
R-4.5-linuxNOTESep 21 2024
R-4.4-winNOTESep 21 2024
R-4.4-macNOTESep 21 2024
R-4.3-winOKSep 21 2024
R-4.3-macOKSep 21 2024

Exports:attriColorGeneattriColorValueattriColorVectorattriShape2GeneattriShape2NodebioCancerCGDScheckDimensionscoffeewheelcoffeewheelOutputdisplayTableEdges_Diseases_objfindPhantomgetEvidenceCodesgetFreqMutDatagetGenesClassificationgetList_CasesgetList_GenProfsgetListProfDatagetOrthologsgetProfDatagetSequensed_SampleSizemapListsmetabologrammetabologramOutputMutation_objNode_df_FreqInNode_Diseases_objNode_obj_CNA_ProfDataNode_obj_FreqInNode_obj_Met_ProfDataNode_obj_mRNA_ClassifierpickGOpickRefSeqremoveNAsrenderCoffeewheelrenderMetabologramreStrColorGenereStrDimensionreStrDiseaseStudies_objtest.CGDStranslateUnifyRowNameswhichGeneListwidgetThumbnail

Dependencies:abindAlgDesignAnnotationDbiAnVILAnVILBaseapeaplotarrowaskpassassertthatbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbootbroombslibcachemcarcarDatacBioPortalDatacellrangerclassclicliprclusterclusterProfilercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDerivDiagrammeRdigestdoByDOSEdplyrDTe1071EBarraysenrichplotevaluatefansifarverfastmapfastmatchfgseafilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsgeNetClassifierGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicDataCommonsGenomicFeaturesGenomicRangesggforceggfunggnewscaleggplot2ggplotifyggraphggrepelggtreeglueGO.dbGOSemSimGPArotationgraphgraphitegraphlayoutsgridExtragridGraphicsgsongtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphimportinfotheoIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelme4lubridatemagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminetminiUIminqamnormtmodelrMultiAssayExperimentmunsellnlmenloptrnnetnumDerivopensslorg.Bt.eg.dborg.Hs.eg.dbpatchworkpbkrtestpillarpkgconfigplogrplotlyplyrpngpolyclipprettyunitsprogresspromisesproxypsychpurrrquantregqvalueR.methodsS3R.ooR.utilsR6radiant.dataRaggedExperimentrandomizrrapiclientrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreactome.dbReactomePAreadrreadxlrematchreshape2restfulrRhtslibrjsonRJSONIOrlangrmarkdownRsamtoolsRSQLiterstudioapiRTCGAToolboxrtracklayerrvestS4ArraysS4VectorssassscalesscatterpieselectrshadowtextshinyshinyAceshinyFilesshinythemessnowsourcetoolsSparseArraySparseMstringistringrSummarizedExperimentsurvivalsyssystemfontsTCGAutilstibbletidygraphtidyrtidyselecttidytreetimechangetinytextreeiotweenrtzdbUCSC.utilsutf8vctrsviridisviridisLitevisNetworkvroomwithrwritexlxfunXMLxml2xtableXVectoryamlyulab.utilszlibbioc

bioCancer: Interactive Multi-OMICS Cancers Data Visualization and Analysis

\ Karim Mezhoud \ \ Nuclear Science Center of Tunisia, Nuclear Safety & Security Department

Rendered frombioCancer.Rmdusingknitr::rmarkdownon Sep 21 2024.

Last update: 2023-09-29
Started: 2016-05-20

Readme and manuals

Help Manual

Help pageTopics
Private Escape string.dbEscapeString
Gets the table name from the INPARANOID style genus names..getTableName
Secret function that does the magic for pickRefSeq..pickRef
Annotation translation functionsAnnotationFuncs
Attribute Color to GeneattriColorGene
Attribute Color to ValueattriColorValue
Attribute color to a vector of numeric valuesattriColorVector
Attribute shape to nodesattriShape2Gene
Attributes shape to NodesattriShape2Node
Launch bioCancer with default browser-package bioCancer
CGDS connect object to cBioPortalCGDS
Check wich Cases and genetic profiles are available for selected studycheckDimensions
This is an htmlwidgets-based visualization tool for hierarchical data. It is zoomable, meaning that you can interact with the hierarchy and zoom in/out accordingly.coffeewheel
Widget output function for use in ShinycoffeewheelOutput
Display dataframe in table using DT packagedisplayTable
get Edges dataframe for Gene/Disease association from geNetClassifierEdges_Diseases_obj
Default dataset of bioCancerepiGenomics
Check if PhantomJS is installed. Similar to webshotfindPhantom
Returns GO evidence codes.getEvidenceCodes
get mutation frequencygetFreqMutData
get genes classificationgetGenesClassification
get list of cases of each selected study in Classifier panelgetList_Cases
get list of genetic profiles of each selected study in Classifier panelgetList_GenProfs
get list of data frame with profiles data (CNA,mRNA, Methylation, Mutation...)getListProfData
Performs quicker lookup for orthologs in homologe data packagesgetOrthologs
search and get genetic profiles (CNA,mRNA, Methylation, Mutation...)getProfData
get samples size of sequensed genesgetSequensed_SampleSize
Replaces contents of list A with elements of list BmapLists
Circular plot of hierarchital data of genetic profile.metabologram
Widget output function for use in ShinymetabologramOutput
Atribute mutation frequency to nodesMutation_obj
Attributes size to Nodes depending on number of interactionNode_df_FreqIn
Attributes color and shape to Nodes of DiseasesNode_Diseases_obj
Attribute CNA data to node borderNode_obj_CNA_ProfData
Attribute interaction frequency to node sizeNode_obj_FreqIn
Attribute gene Methylation to NodesNode_obj_Met_ProfData
Atrribute genes expression to color nodesNode_obj_mRNA_Classifier
Cleans up result from org.Xx.egGO and returns specific GO identifierspickGO
Picks a prioritised RefSeq identifier from a list of identifierspickRefSeq
Removes entries equal 'NA' from list or vectorremoveNAs
Widget render function for use in ShinyrenderCoffeewheel
Widget render function for use in ShinyrenderMetabologram
Restructure the list of color attributed to the genes in every dimenssion for every studiesreStrColorGene
Restructure the list of color attributed to the genes in every study for every dimensionsreStrDimension
Restructure the list of color attributed to the genes in every diseasereStrDisease
Return message when the filter formula is not correct (mRNA > 500)returnTextAreaInput
get object for grViz. Link Studies to genesStudies_obj
A function to change the Original checkbox of rshiny into a nice true/false or on/off switch button No javascript involved. Only CSS code.switchButton
S3 method to test cBioPortal connectiontest.CGDS
Translate between different identifierstranslate
Unify row names in data frame with the same order of gene list.UnifyRowNames
Example of Copy Number Alteration (CNA) datasetuser_CNA
Example of Methylation HM27 datasetuser_MetHM27
Example of Methylation HM450 datasetuser_MetHM450
Example of mRNA expression datasetuser_mRNA
Example of Mutation datasetuser_Mut
Verify which gene list is selectedwhichGeneList
Capture html output widget as .png in RwidgetThumbnail