{ "_id": "6a19efdc1d7bb097a09c93db", "Package": "canceR", "Type": "Package", "Title": "A Graphical User Interface for accessing and modeling the Cancer\nGenomics Data of MSKCC", "Version": "1.47.0", "Date": "2024-02-28", "Author": "Karim Mezhoud. Nuclear Safety & Security Department. Nuclear\nScience Center of Tunisia.", "Maintainer": "Karim Mezhoud ", "Description": "The package is user friendly interface based on the cgdsr\nand other modeling packages to explore, compare, and analyse\nall available Cancer Data (Clinical data, Gene Mutation, Gene\nMethylation, Gene Expression, Protein Phosphorylation, Copy\nNumber Alteration) hosted by the Computational Biology Center\nat Memorial-Sloan-Kettering Cancer Center (MSKCC).", "License": "GPL-2", "LazyLoad": "yes", "SystemRequirements": "Tktable, BWidget", "VignetteBuilder": "knitr", "BugReports": "https://github.com/kmezhoud/canceR/issues", "biocViews": "GUI, GeneExpression, Clustering, GO, GeneSetEnrichment,\nKEGG, MultipleComparison", "RoxygenNote": "7.3.1", "Encoding": "UTF-8", "Config/pak/sysreqs": "bwidget cmake make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libsecret-1-dev libuv1-dev libxml2-dev\nlibssl-dev tk-table libx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:40:44 UTC", "RemoteUrl": "https://github.com/bioc/canceR", "RemoteRef": "HEAD", "RemoteSha": "f1040a48b1dee24114afc8187767d316cc3296fd", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 19:36:59 UTC", "User": "root" }, "MD5sum": "203825322a5d9613ba04bc61225973c0", "_user": "bioc", "_type": "src", "_file": "canceR_1.47.0.tar.gz", "_fileid": "b3ca7a02564080b4363cbf8a0ebc03b834989ea37258f8dfb31dbd383a231374", "_filesize": 32936945, "_sha256": "b3ca7a02564080b4363cbf8a0ebc03b834989ea37258f8dfb31dbd383a231374", "_created": "2026-05-29T19:36:59.000Z", "_published": "2026-05-29T19:58:20.680Z", "_jobs": [ { "job": 78573943138, "time": 371, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7299605114" }, { "job": 78573943220, "time": 632, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7299683794" }, { "job": 78573943208, "time": 772, "config": "linux-release-x86_64", "r": "4.6.0", "check": 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threshold", "topics": [ "dialogGeneClassifier" ] }, { "page": "dialoggetGeneListMSigDB", "title": "Multi-select choice of gene sets from loaded MSigDB", "topics": [ "dialoggetGeneListMSigDB" ] }, { "page": "dialogMetOption", "title": "Dialog Box to set methylation options", "topics": [ "dialogMetOption" ] }, { "page": "dialogMut", "title": "Dialog bos to set returned Mutation information", "topics": [ "dialogMut" ] }, { "page": "dialogOptionCircos", "title": "Checkbox to select dimensions", "topics": [ "dialogOptionCircos" ] }, { "page": "dialogOptionGSEAlm", "title": "Dialogbox to select variables from Clinical data", "topics": [ "dialogOptionGSEAlm" ] }, { "page": "dialogOptionPhenoTest", "title": "Checkbox to select variables from clinical data", "topics": [ "dialogOptionPhenoTest" ] }, { "page": "dialogPlotOption_SkinCor", "title": "Checkbox to select variables for plotting", "topics": [ "dialogPlotOption_SkinCor" ] }, { "page": "dialogSamplingGSEA", "title": "Dialog Box for Sampling patients from expression profile data used for GSEA-R (Broad Institute)", "topics": [ "dialogSamplingGSEA" ] }, { "page": "dialogSelectFiles_GSEA", "title": "Dialog Box to Select GCT, CLS, GMT and output Files for GSEA-R (Broad Institute)", "topics": [ "dialogSelectFiles_GSEA" ] }, { "page": "dialogSpecificMut", "title": "dialog box to Specify Mutation using Regular Expression. Search specific mutation using regular expression.", "topics": [ "dialogSpecificMut" ] }, { "page": "dialogSummary_GSEA", "title": "Dialog Box to specify phenotype (variable) used in last GSEA-R to get Summary Results. This function ask the user to specify the phenotype (variable).", "topics": [ "dialogSummary_GSEA" ] }, { "page": "displayInTable", "title": "Display matrix in tcltk table", "topics": [ "displayInTable" ] }, { "page": "getCases", "title": "Get cases for selected Studies. The Cases are the descrption of the samples from patients. The samples can be subdivided by the type of assays as, sequencing, CNA, Mutation, Methylation.", "topics": [ "getCases" ] }, { "page": "getCasesGenProfs", "title": "get Cases and Genetic Profiles of selected Studies.", "topics": [ "getCasesGenProfs" ] }, { "page": "getCircos", "title": "get Circos Layout for selected studies and selected dimensions", "topics": [ "getCircos" ] }, { "page": "getClinicalDataMatrix", "title": "get matrix with clinical from file", "topics": [ "getClinicalDataMatrix" ] }, { "page": "getClinicData_MultipleCases", "title": "get Clinical Data for Multiple Cases. User needs to select at least one case to run this function. Get clinical data for more one or multiple cases.", "topics": [ "getClinicData_MultipleCases" ] }, { "page": "getCor_ExpCNAMet", "title": "Get gene correlation for multiple dimensions.", "topics": [ "getCor_ExpCNAMet" ] }, { "page": "geteSet", "title": "Built Expression Set (eSet) from profile data.", "topics": [ "geteSet" ] }, { "page": "getFreqMutData", "title": "get mutation frequency", "topics": [ "getFreqMutData" ] }, { "page": "getGCT_CLSfiles", "title": "get Profile (GCT file) and Phenotype (CLS file) Data from Disease.", "topics": [ "getGCT_CLSfiles" ] }, { "page": "getGCTCLSExample", "title": "get GCT and CLS example files.", "topics": [ "getGCTCLSExample" ] }, { "page": "getGeneExpMatrix", "title": "get matrix with gene expression from file", "topics": [ "getGeneExpMatrix" ] }, { "page": "getGeneList", "title": "User needs to specify which gene is interesting to get genomic cancer data. The gene must be with Symbol and one gene by line.", "topics": [ "getGeneList" ] }, { "page": "getGeneListExample", "title": "get Gene List from examples. User can select one from available gene list", "topics": [ "getGeneListExample" ] }, { "page": "getGeneListFromMSigDB", "title": "get gene list from MSigDB", "topics": [ "getGeneListFromMSigDB" ] }, { "page": "getGenesClassifier", "title": "get Genes Classifier", "topics": [ "getGenesClassifier" ] }, { "page": "getGenesTree_MultipleCases", "title": "Get successively trees of genes list for multiple cases", "topics": [ "getGenesTree_MultipleCases" ] }, { "page": "getGenesTree_SingleCase", "title": "classify genes in tree for two phenotypes in the same case(disease).", "topics": [ "getGenesTree_SingleCase" ] }, { "page": "getGenProfs", "title": "Get Genetic Profile from selected Studies", "topics": [ "getGenProfs" ] }, { "page": "getGSEAlm_Diseases", "title": "get GSEA linear modeling by studies (diseases)", "topics": [ "getGSEAlm_Diseases" ] }, { "page": "getGSEAlm_Variables", "title": "get GSEA linear modeling by variables (phenotype)", "topics": [ "getGSEAlm_Variables" ] }, { "page": "getInTable", "title": "get dataframe in TK/TCL table", "topics": [ "getInTable" ] }, { "page": "getListProfData", "title": "Get list of data frame with profiles data (CNA,mRNA, Methylation, Mutation...)", "topics": [ "getListProfData" ] }, { "page": "getMegaProfData", "title": "Get profile data for more than 500 genes list.", "topics": [ "getMegaProfData" ] }, { "page": "getMetDataMultipleGenes", "title": "get Methylation data for multiple genes", "topics": [ "getMetDataMultipleGenes" ] }, { "page": "getMSigDB", "title": "Reduce MSigDB size for only gene list", "topics": [ "getMSigDB" ] }, { "page": "getMSigDBExample", "title": "get example of .gmt file from MSigDB (Broad Institute)", "topics": [ "getMSigDBExample" ] }, { "page": "getMSigDBfile", "title": "Dialog Box to Select MSigDB Files from drive", "topics": [ "getMSigDBfile" ] }, { "page": "getMutData", "title": "get Mutation data for multiple genes", "topics": [ "getMutData" ] }, { "page": "getPhenoTest", "title": "Associate phenotype to Studies (cancers)", "topics": [ "getPhenoTest" ] }, { "page": "getProfData", "title": "Search and get genetic profiles (CNA,mRNA, Methylation, Mutation...)", "topics": [ "getProfData" ] }, { "page": "getProfilesDataMultipleGenes", "title": "get Profles Data of multiple genes", "topics": [ "getProfilesDataMultipleGenes" ] }, { "page": "getProfilesDataSingleGene", "title": "get Profiles Data for a Single Gene.", "topics": [ "getProfilesDataSingleGene" ] }, { "page": "getSpecificMut", "title": "get specific Mutation data for multiple genes", "topics": [ "getSpecificMut" ] }, { "page": "getSummaryGSEA", "title": "get Summary results from GSEA-R (Broad Institute)", "topics": [ "getSummaryGSEA" ] }, { "page": "getSurvival", "title": "Survival plot", "topics": [ "getSurvival" ] }, { "page": "getTextWin", "title": "get text in tcltk windows", "topics": [ "getTextWin" ] }, { "page": "GSEA", "title": "GSEA-R (Broad Institute)", "topics": [ "GSEA" ] }, { "page": "GSEA.Analyze.Sets", "title": "GSEA.Analyze.Sets", "topics": [ "GSEA.Analyze.Sets" ] }, { "page": "GSEA.ConsPlot", "title": "GSEA.ConsPlot", "topics": [ "GSEA.ConsPlot" ] }, { "page": "GSEA.EnrichmentScore", "title": "GSEA.EnrichmentScore", "topics": [ "GSEA.EnrichmentScore" ] }, { "page": "GSEA.EnrichmentScore2", "title": "GSEA.EnrichmentScore2", "topics": [ "GSEA.EnrichmentScore2" ] }, { "page": "GSEA.Gct2Frame", "title": "GSEA.Gct2Frame", "topics": [ "GSEA.Gct2Frame" ] }, { "page": "GSEA.Gct2Frame2", "title": "GSEA.Gct2Frame2", "topics": [ "GSEA.Gct2Frame2" ] }, { "page": "GSEA.GeneRanking", "title": "GSEA.GeneRanking", "topics": [ "GSEA.GeneRanking" ] }, { "page": "GSEA.HeatMapPlot", "title": "GSEA.HeatMapPlot", "topics": [ "GSEA.HeatMapPlot" ] }, { "page": "GSEA.HeatMapPlot2", "title": "GSEA.HeatMapPlot2", "topics": [ "GSEA.HeatMapPlot2" ] }, { "page": "GSEA.NormalizeCols", "title": "GSEA.NormalizeCols", "topics": [ "GSEA.NormalizeCols" ] }, { "page": "GSEA.NormalizeRows", "title": "GSEA.NormalizeRows", "topics": [ "GSEA.NormalizeRows" ] }, { "page": "GSEA.ReadClsFile", "title": "GSEA.ReadClsFile", "topics": [ "GSEA.ReadClsFile" ] }, { "page": "GSEA.Res2Frame", "title": "GSEA.Res2Frame", "topics": [ "GSEA.Res2Frame" ] }, { "page": "GSEA.Threshold", "title": "GSEA.Threshold", "topics": [ "GSEA.Threshold" ] }, { "page": "GSEA.VarFilter", "title": "GSEA.VarFilter", "topics": [ "GSEA.VarFilter" ] }, { "page": "GSEA.write.gct", "title": "GSEA.write.gct", "topics": [ "GSEA.write.gct" ] }, { "page": "Match_GeneList_MSigDB", "title": "Search MSigDb that overlap gene list", "topics": [ "Match_GeneList_MSigDB" ] }, { "page": "modalDialog", "title": "Dialog box to specify Gene Symbol.", "topics": [ "modalDialog" ] }, { "page": "myGlobalEnv", "title": "myGlobalEnv", "topics": [ "myGlobalEnv" ] }, { "page": "OLD.GSEA.EnrichmentScore", "title": "OLD.GSEA.EnrichmentScore", "topics": [ "OLD.GSEA.EnrichmentScore" ] }, { "page": "plot_1Gene_2GenProfs", "title": "Plotting two genetic profiles for one Gene", "topics": [ "plot_1Gene_2GenProfs" ] }, { "page": "plot_2Genes_1GenProf", "title": "plot correlation of two genes expressions.", "topics": [ "plot_2Genes_1GenProf" ] }, { "page": "plotModel", "title": "model plotting with tcltk", "topics": [ "plotModel" ] }, { "page": "rbind.na", "title": "bind non equal row", "topics": [ "rbind.na" ] }, { "page": "Run.GSEA", "title": "The main function to run GSEA-R from Broad Institute", "topics": [ "Run.GSEA" ] }, { "page": "setWorkspace", "title": "Setting work Directory and output folders.At starting window, user needs to set work directory for output data. The function is foud in File menu.", "topics": [ "setWorkspace" ] }, { "page": "test.CGDS", "title": "S3 method to test cBioPortal connection", "topics": [ "test.CGDS" ] }, { "page": "testCheckedCaseGenProf", "title": "Testing checked appropriate Cases for appropriate Genetic profiles.", "topics": [ "testCheckedCaseGenProf" ] }, { "page": "UnifyRowNames", "title": "Unify row names in data frame with the same order of gene list.", "topics": [ "UnifyRowNames" ] } ], "_readme": "https://github.com/bioc/canceR/raw/HEAD/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "AnVIL", "AnVILBase", "askpass", "backports", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "BMA", "bslib", "cachem", "Category", "caTools", "cBioPortalData", "checkmate", "cigarillo", "circlize", "class", "cli", "clipr", "cluster", "codetools", "colorspace", "commonmark", "cpp11", "crayon", 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accessing and modeling the Cancer Genomics Data of MSKCC", "author": "Karim Mezhoud", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Suplementary librairies (Not R packages)", "dependencies from Bioconductor", "Starting Window", "Setting Workspace", "Main Window", "Gene List", "Clinical Data", "Mutation", "Methylation", "Profiles", "PhenoTest", "Examples", "GSEA-R", "Preprocessing of Exprimental Data", "Molecular Signatures DataBase", "MSigDB Collection", "Study: Uterine Corpus Endometrioid Carcinoma (TCGA, Nature 2013)", "Study: Breast Invasive Carcinoma (TCGA, Provosional)", "GSEA-R Result Interpretation", "Resolved limits", "Linear Modeling of GSEA (GSEAlm)", "Results interpretation:", "Limitations:", "Which Molecular Signature Data base (MSigDB) for gene list", "get SubMSigDb for genes list", "GSEAlm: Phenotypes into Disease", "Disease Free Status (DFS_STATUS) into Prostate Cancer:", "Copy Number Cluster Level into Stomach Adenocarcinoma:", "GSEAlm: Disease vs Disease}", "Breast vs Prostate Cancers:", "Genes Classification using mRNA expression (Classification)", "Genes vs Diseases (inter-diseases)", "Example 1: Breast vs Glioblastoma vs Liver vs Lung Cancers (Figure~@ref(fig:GenesClass)A):}", "Example 2: Bladder vs Breast vs Glioblastoma vs Lung vs Ovarian vs Prostate Cancers (Figure~\\ref", "Genes vs Phenotypes (intra-disease)", "Example 1: Genes classification vs OS_STATUS (Living/Deceased)", "Example 2: Genes regression vs OS_STATUS (Living/Deceased)", "Example 3: Genes classification vs tumor grade (grade1/2/3)", "Plots", "Example: Association of P53 copy number alteration and mRNA exprssion in glioblastoma", "Example: MAP2K2 and ABHD17A mRNA expression (RNA Seq V2 RSEM) levels in Uterine Corpus Endometrioid Carcinoma (TCGA, Nature 2013)", "Survival Plots", "Kaplan-Meier Curves", "Cox proportional Hazards Model", "Circos Style", "References" ], "created": "2022-04-24 22:17:59", "modified": "2022-04-24 22:17:59", "commits": 1 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