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| colDataPrepare | Create samples information matrix for GDC samples |
| dmc.non.parametric | Perform non-parametrix wilcoxon test |
| gaiaCNVplot | Creates a plot for GAIA output (all significant aberrant regions.) |
| GDCdownload | Download GDC data |
| GDCprepare | Prepare GDC data |
| GDCprepare_clinic | Parsing clinical xml files |
| GDCquery | Query GDC data |
| GDCquery_ATAC_seq | Retrieve open access ATAC-seq files from GDC server |
| GDCquery_clinic | Get GDC clinical data |
| GDCquery_Maf | Retrieve open access maf files from GDC server |
| get.GRCh.bioMart | Get hg19 or hg38 information from biomaRt |
| getAdjacencyBiogrid | Get a matrix of interactions of genes from biogrid |
| getDataCategorySummary | Create a Summary table for each sample in a project saying if it contains or not files for a certain data category |
| getGDCInfo | Check GDC server status |
| getGDCprojects | Retrieve all GDC projects |
| getGistic | Download GISTIC data from firehose |
| getLinkedOmicsData | Retrieve linkedOmics data |
| getManifest | Get a Manifest from GDCquery output that can be used with GDC-client |
| getMC3MAF | Retrieve open access mc3 MAF file from GDC server |
| getNbCases | Get Number of cases in GDC for a project |
| getNbFiles | Get Number of files in GDC for a project |
| getProjectSummary | Get Project Summary from GDC |
| getResults | Get the results table from query |
| getSampleFilesSummary | Retrieve summary of files per sample in a project |
| getTSS | getTSS to fetch GENCODE gene annotation (transcripts level) from Bioconductor package biomaRt If upstream and downstream are specified in TSS list, promoter regions of GENCODE gene will be generated. |
| get_IDs | Extract information from TCGA barcodes. |
| gliomaClassifier | Gliomar classifier |
| isServeOK | Check GDC server status is OK |
| matchedMetExp | Get GDC samples with both DNA methylation (HM450K) and Gene expression data from GDC databse |
| PanCancerAtlas_subtypes | Retrieve table with TCGA molecular subtypes |
| splitAPICall | internal function to break a huge API call into smaller ones so it repects the max character limit of a string |
| TabSubtypesCol_merged | TCGA samples with their Pam50 subtypes |
| TCGAanalyze_analyseGRN | Generate network |
| TCGAanalyze_Clustering | Hierarchical cluster analysis |
| TCGAanalyze_DEA | Differential expression analysis (DEA) using edgeR or limma package. |
| TCGAanalyze_DEA_Affy | Differentially expression analysis (DEA) using limma package. |
| TCGAanalyze_DMC | Differentially methylated regions Analysis |
| TCGAanalyze_EA | Enrichment analysis of a gene-set with GO [BP,MF,CC] and pathways. |
| TCGAanalyze_EAcomplete | Enrichment analysis for Gene Ontology (GO) [BP,MF,CC] and Pathways |
| TCGAanalyze_Filtering | Filtering mRNA transcripts and miRNA selecting a threshold. |
| TCGAanalyze_LevelTab | Adding information related to DEGs genes from DEA as mean values in two conditions. |
| TCGAanalyze_networkInference | infer gene regulatory networks |
| TCGAanalyze_Normalization | normalization mRNA transcripts and miRNA using EDASeq package. |
| TCGAanalyze_Pathview | Generate pathview graph |
| TCGAanalyze_Preprocessing | Array Array Intensity correlation (AAIC) and correlation boxplot to define outlier |
| TCGAanalyze_Stemness | Generate Stemness Score based on RNASeq (mRNAsi stemness index) Malta et al., Cell, 2018 |
| TCGAanalyze_survival | Creates survival analysis |
| TCGAanalyze_SurvivalKM | survival analysis (SA) univariate with Kaplan-Meier (KM) method. |
| TCGAbatch_Correction | Batch correction using ComBat and Voom transformation using limma package. |
| TCGAbiolinks | The aim of TCGAbiolinks is : i) facilitate the TCGA open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) allow the user to download a specific version of the data and thus to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines. |
| TCGAprepare_Affy | Prepare CEL files into an AffyBatch. |
| TCGAquery_MatchedCoupledSampleTypes | Retrieve multiple tissue types from the same patients. |
| TCGAquery_recount2 | Query gene counts of TCGA and GTEx data from the Recount2 project |
| TCGAquery_SampleTypes | Retrieve multiple tissue types not from the same patients. |
| TCGAquery_subtype | Retrieve molecular subtypes for a given tumor |
| TCGAtumor_purity | Filters TCGA barcodes according to purity parameters |
| TCGAvisualize_BarPlot | Barplot of subtypes and clinical info in groups of gene expression clustered. |
| TCGAvisualize_EAbarplot | barPlot for a complete Enrichment Analysis |
| TCGAvisualize_Heatmap | Heatmap with more sensible behavior using heatmap.plus |
| TCGAvisualize_meanMethylation | Mean methylation boxplot |
| TCGAvisualize_oncoprint | Creating a oncoprint |
| TCGAvisualize_PCA | Principal components analysis (PCA) plot |
| TCGAvisualize_starburst | Create starburst plot |
| TCGAvisualize_SurvivalCoxNET | Survival analysis with univariate Cox regression package (dnet) |
| TCGAVisualize_volcano | Creates a volcano plot for DNA methylation or expression |
| TCGA_MolecularSubtype | Retrieve molecular subtypes for given TCGA barcodes |
| Tumor.purity | TCGA samples with their Tumor Purity measures |
| UseRaw_afterFilter | Use raw count from the DataPrep object which genes are removed by normalization and filtering steps. |