Man pages for BioinformaticsFMRP/TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
| batch.info | TCGA batch information from Biospecimen Metadata Browser |
| bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.maf | TCGA CHOL MAF |
| chol_maf | TCGA CHOL MAF transformed to maftools object |
| classification | Result of gliomaclassifier function |
| clinBRCA | Clinical data TCGA BRCA |
| clinical.biotab | A list of data frames with clinical data parsed from XML... |
| colDataPrepare | Create samples information matrix for GDC samples |
| dataBRCA | TCGA data matrix BRCA |
| dataDEGsFiltLevel | TCGA data matrix BRCA DEGs |
| dataREAD | TCGA data SummarizedExperiment READ |
| dataREAD_df | TCGA data matrix READ |
| DE_PCBC_stemSig | A numeric vector with SC-derived definitive endoderm (DE)... |
| dmc.non.parametric | Perform non-parametrix wilcoxon test |
| dmc.non.parametric.se | Calculate pvalues |
| EB_PCBC_stemSig | A numeric vector with stem cell (SC)-derived embryoid bodies... |
| ECTO_PCBC_stemSig | A numeric vector with SC-derived ectoderm (ECTO) signature... |
| gaiaCNVplot | Creates a plot for GAIA output (all significant aberrant... |
| gbm.exp.harmonized | A RangedSummarizedExperiment two samples with gene expression... |
| gbm.exp.legacy | A RangedSummarizedExperiment two samples with gene expression... |
| 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 |
| geneInfo | geneInfo for normalization of RNAseq data |
| geneInfoHT | geneInfoHT for normalization of HTseq data |
| GenesCutID | GenesCutID |
| GeneSplitRegulon | GeneSplitRegulon |
| getAdjacencyBiogrid | Get a matrix of interactions of genes from biogrid |
| getDataCategorySummary | Create a Summary table for each sample in a project saying if... |
| getGDCInfo | Check GDC server status |
| getGDCprojects | Retrieve all GDC projects |
| getGistic | Download GISTIC data from firehose |
| get.GRCh.bioMart | Get hg19 gene annotation or hg38 (gencode v36) |
| get_IDs | Extract information from TCGA barcodes. |
| getLinkedOmicsData | Retrieve linkedOmics data |
| getManifest | Get a Manifest from GDCquery output that can be used with... |
| 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)... |
| ggbiplot | Biplot for Principal Components using ggplot2 |
| gliomaClassifier | Gliomar classifier |
| isServeOK | Check GDC server status is OK |
| matchedMetExp | Get GDC primary tumors samples with both DNA methylation... |
| MESO_PCBC_stemSig | A numeric vector with SC-derived mesoderm (MESO) signature... |
| met.gbm.27k | A DNA methylation RangedSummarizedExperiment for 8 samples... |
| msi_results | MSI data for two samples |
| pancan2018 | A data frame with all TCGA molecular subtypes |
| PanCancerAtlas_subtypes | Retrieve table with TCGA molecular subtypes |
| SC_PCBC_stemSig | A numeric vector with stem cell-like signature trained on... |
| splitAPICall | internal function to break a huge API call into smaller ones... |
| TabSubtypesCol_merged | TCGA samples with their Pam50 subtypes |
| tabSurvKMcompleteDEGs | tabSurvKMcompleteDEGs |
| TCGAanalyze_analyseGRN | Generate network |
| TCGAanalyze_Clustering | Hierarchical cluster analysis |
| TCGAanalyze_DEA | Differential expression analysis (DEA) using edgeR or limma... |
| 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... |
| TCGAanalyze_EAcomplete | Enrichment analysis for Gene Ontology (GO) [BP,MF,CC] and... |
| TCGAanalyze_Filtering | Filtering mRNA transcripts and miRNA selecting a threshold. |
| TCGAanalyze_LevelTab | Adding information related to DEGs genes from DEA as mean... |
| TCGAanalyze_networkInference | infer gene regulatory networks |
| TCGAanalyze_Normalization | normalization mRNA transcripts and miRNA using EDASeq... |
| TCGAanalyze_Pathview | Generate pathview graph |
| TCGAanalyze_Preprocessing | Array Array Intensity correlation (AAIC) and correlation... |
| TCGAanalyze_Stemness | Generate Stemness Score based on RNASeq (mRNAsi stemness... |
| TCGAanalyze_survival | Creates survival analysis |
| TCGAanalyze_SurvivalKM | survival analysis (SA) univariate with Kaplan-Meier (KM)... |
| TCGAbatch_Correction | Batch correction using ComBat and Voom transformation using... |
| TCGAbiolinks-package | The aim of TCGAbiolinks is : i) facilitate the TCGA... |
| TCGA_MolecularSubtype | Retrieve molecular subtypes for given TCGA barcodes |
| 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... |
| 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... |
| 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... |
| TCGAVisualize_volcano | Creates a volcano plot for DNA methylation or gene expression |
| Tumor.purity | TCGA samples with their Tumor Purity measures |
| UseRaw_afterFilter | Use raw count from the DataPrep object which genes are... |
