Useful information | Searching arguments | project options | sample.type options | Harmonized data options | Harmonized database examples | DNA methylation data: Recurrent tumor samples | Samples with DNA methylation and gene expression data | Raw Sequencing Data: Finding the match between file names and barcode for Controlled data. | Get Manifest file | ATAC-seq data | Summary of available files per patient

Classifying gliomas samples with gliomaClassifier | Data | Function | Results | Comparing results with paper

Data Introduction | Loading the data | Data creation | Genes information | GISTIC results | Gene expression data | DNA methylation and Gene expression data | Mutation data | Biogrid data | Histone marks | Session info

Useful information | BCR Biotab | Clinical | Biospecimen | Clinical indexed data | XML clinical data | Diagnostic Slide (SVS format) | Filter functions | Other useful code

Search and Download | Mutation data (hg38) | Mutation data MC3 file | Visualize the data

TCGAanalyze: Analyze data from TCGA. | TCGAanalyze_Preprocessing: Preprocessing of Gene Expression data (IlluminaHiSeq_RNASeqV2) | TCGAanalyze_DEA & TCGAanalyze_LevelTab: Differential expression analysis (DEA) | HTSeq data: Downstream analysis BRCA | miRNA expression data: Downstream analysis BRCA | TCGAanalyze_EAcomplete & TCGAvisualize_EAbarplot: Enrichment Analysis | TCGAanalyze_survival: Survival Analysis | TCGAanalyze_SurvivalKM: Correlating gene expression and Survival Analysis | TCGAanalyze_DMR: Differentially methylated regions Analysis | TCGAvisualize: Visualize results from analysis functions with TCGA's data. | TCGAvisualize_Heatmap: Create heatmaps with cluster bars | TCGAvisualize_Volcano: Create volcano plot | TCGAvisualize_PCA: Principal Component Analysis plot for differentially expressed genes | TCGAvisualize_meanMethylation: Mean DNA Methylation Analysis | TCGAvisualize_starburst: Integration of gene expression and DNA methylation data | Session Information

Downloading and preparing data for analysis | Arguments | GDCdownload | GDCprepare | Search and download data for two samples from database | GDCprepare: Outputs | Harmonized data | Examples | Harmonized database: data aligned against hg38 | Copy Number Variation | Copy Number Segment | Gene Level Copy Number | Allele-specific Copy Number Segment | Masked Copy Number Segment | Transcriptome Profiling | Gene Expression Quantification | miRNA Expression Quantification | Isoform Expression Quantification | DNA methylation | Beta-values | IDAT files | Proteome Profiling | Protein Expression Quantification | Clinical | Simple Nucleotide Variation | Masked Somatic Mutation | Single cell

PanCancerAtlas_subtypes: Curated molecular subtypes. | TCGAquery_subtype: Working with molecular subtypes data. | Session Information

Introduction | Case study n. 1: Pan Cancer downstream analysis BRCA | Case study n. 2: Pan Cancer downstream analysis LGG | Case study n. 3: Integration of methylation and expression for ACC | Case study n. 4: ELMER pipeline - KIRC | Session Information | References

Calculate stemness score with TCGAanalyze_Stemness | Data | Function | Output

News | Citation | Other useful links | Installation | Question and issues | Required libraries | Session info

Support of Therapeutically Applicable Research To Generate Effective Treatments (TARGET) data: | Querying, downloading, and preparing TARGET data: | Preparing BRCA data for downstream analysis: Differential Expression Analysis | UseRaw_afterFilter: Keep raw counts after filtering | TCGA_MolecularSubtype: Query subtypes for cancer data: | Differential expression analysis with TCGAanalyze_DEA(): | Limma pipeline | Customization of contrast using ---contrast.formula--- argument: | TCGAbatch_correction: Handle batch correction and lima-voom transformation | TCGAbatch_correction: working with unpublished datasets | TCGAtumor_purity: Filter TCGA samples according to tumor purity | Download GTEx data available through the Recount2 project: