Introduction

This package is for downloading TCGA project data on a managable data structure (see following output structure). Both of hg19 and hg38 version are provided. Please feel free to open up issues if you have any questions.

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Noticce: The TPM/FPKM range between hg19 and hg38 has hug difference.

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Install:

git clone git@github.com:jingxinfu/TCGAdnloader.git
cd TCGAdnloader
pip install .

Usage:

usage: tcgaDnloader [-h] -o OUTPUT [-r REF [REF ...]] [-c CANCER [CANCER ...]]
                    [--no-meta] [--no-drug] [-t DATATYPE [DATATYPE ...]]

Tools to download public genomic data

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        Output directory (default: None)
  -r REF [REF ...], --ref REF [REF ...]
                        Aligned Reference (default: ['hg19', 'hg38'])
  -c CANCER [CANCER ...], --cancer CANCER [CANCER ...]
                        Cancer type included (default: ['ACC', 'BRCA', 'CHOL',
                        'ESCA', 'KICH', 'KIRP', 'LGG', 'LUAD', 'MESO', 'PAAD',
                        'PRAD', 'SARC', 'STAD', 'TGCT', 'THYM', 'UCS', 'BLCA',
                        'CESC', 'COAD', 'DLBC', 'GBM', 'HNSC', 'KIRC', 'LAML',
                        'LIHC', 'LUSC', 'OV', 'PCPG', 'READ', 'SKCM', 'THCA',
                        'UCEC', 'UVM'])
  --no-meta             Do not install meta information (default: True)
  --no-drug             Do not install drug information (default: True)
  -t DATATYPE [DATATYPE ...], --datatype DATATYPE [DATATYPE ...]
                        Data type included (default: ['rnaseq', 'cnv', 'rppa',
                        'snv'])

Output Data Structure:

Overview

(output directory)
├── hg19
│   ├── CNV
│   │   ├── all
│   │   │   └── segment
│   │   └── somatic
│   │       ├── gene
│   │       │   ├── broad_focal
│   │       │   ├── focal
│   │       │   └── threds
│   │       └── segment
│   ├── RNASeq
│   │   ├── count
│   │   │   └── origin
│   │   ├── fpkm
│   │   │   ├── origin
│   │   │   └── zscore_tumor
│   │   ├── norm_count
│   │   │   └── origin
│   │   └── tpm
│   │       ├── origin
│   │       └── zscore_tumor
│   └── RPPA
└── hg38
    ├── CNV
    │   ├── all
    │   │   └── segment
    │   └── somatic
    │       ├── gene
    │       │   └── focal
    │       └── segment
    ├── RNASeq
    │   ├── count
    │   │   └── origin
    │   ├── fpkm
    │   │   ├── origin
    │   │   └── zscore_tumor
    │   ├── fpkm_uq
    │   │   └── origin
    │   └── tpm
    │       ├── origin
    │       └── zscore_tumor
    ├── sample_pheno
    │   ├── origin
    |   ├── normal
    │   └── tumor
    ├── SNV
    │   ├── muse
    │   ├── mutect2
    │   ├── SomaticSnipe
    │   └── VarScan2
    └── Surv

Note:

• CNV

  • broad_focal : Region reaches significance due to either broad or focal event.

• RNA-Seq

  • origin: Files directly downloaded by API

  • zscore_paired :

    1. log2(x+1)

    2. minus the average across normal samples

  • zscore_tumor :

    1. pick up tumor samples

    2. log2(x+1)

    3. minus the average across samples

  • fpkm_uq :

    • A modified version of the FPKM formula in which the 75th percentile read count is used as the denominator in place of the total number of protein-coding reads

• RPPA

  • Only available for hg19

• SNV:

  • Mutation files for hg19 can be downloaded separatly by this url. This is a MC3 results.