TCGAbiolinks-package | Download data of samples from TCGA |
GDCdownload | Download GDC data |
GDCprepare | Prepare GDC data |
GDCprepare_clinic | Parsing clinical xml files |
GDCquery | Query GDC data |
GDCquery_clinic | Get DDC clinical data |
GDCquery_Maf | Retrieve open access maf files from GDC server |
getGDCprojects | Retrieve all GDC projects |
isServeOK | Check GDC server status |
TCGAanalyze_analyseGRN | Generate network |
TCGAanalyze_Clustering | Hierarchical cluster analysis |
TCGAanalyze_DEA | Differentially expression analysis (DEA) using edgeR package. |
TCGAanalyze_DEA_Affy | Differentially expression analysis (DEA) using limma package. |
TCGAanalyze_DMR | 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_Normalization | normalization mRNA transcripts and miRNA using EDASeq package. |
TCGAanalyze_Preprocessing | Array Array Intensity correlation (AAIC) and correlation boxplot to define outlier |
TCGAanalyze_survival | Creates survival analysis |
TCGAanalyze_SurvivalKM | survival analysis (SA) univariate with Kaplan-Meier (KM) method. |
TCGAbiolinks | Download data of samples from TCGA |
TCGAdownload | Download the data from TCGA using as reference the output from TCGAquery |
TCGAprepare | Read the data from level 3 the experiments and prepare it for downstream analysis into a SummarizedExperiment object. |
TCGAprepare_Affy | Prepare CEL files into an AffyBatch. |
TCGAprepare_elmer | Prepare the data for ELEMR package |
TCGAquery | Searches TCGA open-access data providing also latest version of the files. |
TCGAquery_clinic | Get the clinical information |
TCGAquery_clinicFilt | Filter samples using clinical data |
TCGAquery_maf | Get last maf file for the tumor |
TCGAquery_MatchedCoupledSampleTypes | Retrieve multiple tissue types from the same patients. |
TCGAquery_SampleTypes | Retrieve multiple tissue types not from the same patients. |
TCGAquery_subtype | Retrieve molecular subtypes for a given tumor |
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_Tables | Visaulize results in format of latex tables. |
TCGAVisualize_volcano | Creates a volcano plot for DNA methylation or expression |