Pipeline for downloading HARMONIZED transcriptome profiling data from TCGA and TARGET projects using TCGAbiolinks R package. It uses the GDC Data Transfer Tool Client to download the data from the Genomic Data Commons (GDC) portal. The script outputs normalised expression (FPKM or FPKM-UQ) or raw count matrix for RNA-seq data for user-defined tissue types along with associated clinical information.
The TCGA genomic data harmonization is here and the mRNA analysis pipeline is described here.
- Stable version of TCGAbiolinks R package from Bioconductor
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("TCGAbiolinks")
- NOTE, in case of any issues with the stable version, one can try using the development version from GitHub
devtools::install_github('BioinformaticsFMRP/TCGAbiolinks')
For instance, that may be the case when biomaRt is updated and significant changes are introduced to Ensembl BioMart database (see this GitHub post).
| Argument | Short | Description |
|---|---|---|
| --out_dir | -o | Directory to which the data is to be downloaded |
| --project_id | -p | ID of the TCGA/TARGET project to download |
| --tissue | -t | Tissue types to be considered for download |
| --workflow | -w | Workflow from which the data is to be downloaded |
Use the TCGAbiolinks_transcriptome_profiling_data.R script to download read count matrix for pancreatic cancer (PAAD) project.
Rscript TCGAbiolinks_transcriptome_profiling_data.R --out_dir TCGA/PAAD --project_id TCGA-PAAD --tissue 1,11 --workflow Counts
TCGA
|
|____PAAD
|
|____transcriptome_profiling
|
|____Counts
|____Counts.exp
|____Counts_boxplot.pdf
|____Counts_clinical_info.txt
|____Counts_samples.txt
|____gdc-client
|____gdc-client_v1.1.0_OSX_x64.zip
|____gdc_manifest.txt
|____R_parameters.txt
|____GDCdata
|
|____TCGA-PAAD
|
|____harmonized
|
|____Transcriptome_Profiling
| |
| |____Gene_Expression_Quantification
| |____…
| |____…
|
|____Clinical
|
|____Clinical_Supplement
|____…
|____…
| File | Description |
|---|---|
| Counts.exp | Read count data matrix |
| Counts_boxplot.pdf | Box plot of read counts per sample |
| Counts_clinical_info.txt | Samples and associated clinical annotation |
| R_parameters.txt | User-defined parameters used for the script execution |
| Gene_Expression_Quantification | Folder with compressed 'txt' files containing expression values for each sample |
| Clinical_Supplement | Folder with 'xml' files including clinical information for each sample |
Local workspace. This is the directory to which the data will be downloaded and stored.
Available TCGA/TARGET project IDs are:
| Project ID | Name |
|---|---|
| TCGA-SARC | Sarcoma |
| TCGA-MESO | Mesothelioma |
| TCGA-READ | Rectum Adenocarcinoma |
| TCGA-KIRP | Kidney Renal Papillary Cell Carcinoma |
| TARGET-NBL | Neuroblastoma |
| TCGA-PAAD | Pancreatic Adenocarcinoma |
| TCGA-GBM | Glioblastoma Multiforme |
| TCGA-ACC | Adrenocortical Carcinoma |
| TARGET-OS | Osteosarcoma |
| TCGA-CESC | Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma |
| TARGET-RT | Rhabdoid Tumour |
| TCGA-BRCA | Breast Invasive Carcinoma |
| TCGA-ESCA | Esophageal Carcinoma |
| TCGA-DLBC | Lymphoid Neoplasm Diffuse Large B-cell Lymphoma |
| TCGA-KICH | Kidney Chromophobe |
| TCGA-KIRC | Kidney Renal Clear Cell Carcinoma |
| TCGA-UVM | Uveal Melanoma |
| TARGET-AML | Acute Myeloid Leukaemia |
| TCGA-LAML | Acute Myeloid Leukaemia |
| TCGA-SKCM | Skin Cutaneous Melanoma |
| TCGA-PCPG | Pheochromocytoma and Paraganglioma |
| TCGA-COAD | Colon Adenocarcinoma |
| TCGA-UCS | Uterine Carcinosarcoma |
| TCGA-LUSC | Lung Squamous Cell Carcinoma |
| TCGA-LGG | Brain Lower Grade Glioma |
| TCGA-HNSC | Head and Neck Squamous Cell Carcinoma |
| TCGA-TGCT | Testicular Germ Cell Tumours |
| TARGET-CCSK | Clear Cell Sarcoma of the Kidney |
| TCGA-THCA | Thyroid Carcinoma |
| TCGA-LIHC | Liver Hepatocellular Carcinoma |
| TCGA-BLCA | Bladder Urothelial Carcinoma |
| TCGA-UCEC | Uterine Corpus Endometrial Carcinoma |
| TARGET-WT | High-Risk Wilms Tumour |
| TCGA-PRAD | Prostate Adenocarcinoma |
| TCGA-OV | Ovarian Serous Cystadenocarcinoma |
| TCGA-THYM | Thymoma |
| TCGA-CHOL | Cholangiocarcinoma |
| TCGA-STAD | Stomach Adenocarcinoma |
| TCGA-LUAD | Lung Adenocarcinoma |
Multiple tissue types are allowed. Each tissue type is expected to be separated by comma. Type 'all' for all listed tissue types to be considered for download. Available options are:
| Tissue code | Letter code | Definition |
|---|---|---|
| 1 | TP | Primary solid Tumour |
| 2 | TR | Recurrent Solid Tumour |
| 3 | TB | Primary Blood Derived Cancer - Peripheral Blood |
| 4 | TRBM | Recurrent Blood Derived Cancer - Bone Marrow |
| 5 | TAP | Additional - New Primary |
| 6 | TM | Metastatic |
| 7 | TAM | Additional Metastatic |
| 8 | THOC | Human Tumour Original Cells |
| 9 | TBM | Primary Blood Derived Cancer - Bone Marrow |
| 10 | NB | Blood Derived Normal |
| 11 | NT | Solid Tissue Normal |
| 12 | NBC | Buccal Cell Normal |
| 13 | NEBV | EBV Immortalised Normal |
| 14 | NBM | Bone Marrow Normal |
| 20 | CELLC | Control Analyte |
| 40 | TRB | Recurrent Blood Derived Cancer - Peripheral Blood |
| 50 | CELL | Cell Lines |
| 60 | XP | Primary Xenograft Tissue |
| 61 | XCL | Cell Line Derived Xenograft Tissue |
| All | --- | All available tissue types |
Data from three workflows are available:
| Workflow | Definition |
|---|---|
| Counts | Raw Read Counts - the number of reads aligned to each protein-coding gene, calculated by HT-Seq (default) |
| FPKM | Normalised expression value that takes into account each protein-coding gene length and the number of reads mappable to all protein-coding genes |
| FPKM-UQ | Normalised raw read count in which gene expression values, in FPKM, are divided by the 75th percentile value |
Make sure that R version >= 3.3 is installed. For older versions the TCGAbiolinks uses different functions starting with "TCGA" rather than "GDC" since the data were moved from DCC server to NCI Genomic Data Commons (GDC). Make sure that the newest TCGAbiolinks package package is installed.
devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")