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awesome-TCGA

Curated list of TCGA resources
https://github.com/IARCbioinfo/awesome-TCGA

Last synced: about 20 hours ago
JSON representation

    • General informations

      • NCI TCGA Wiki - General help about TCGA project. One page you may visit often is the [TCGA barcode](https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode) description.
      • Data documentation - Describe how the data is generated, in particular the details of the bioinformatics pipeline used.
      • NCI TCGA Wiki - General help about TCGA project. One page you may visit often is the [TCGA barcode](https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode) description.
      • NCI TCGA Wiki - General help about TCGA project. One page you may visit often is the [TCGA barcode](https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode) description.

    • Data repositories

  • Downloading the data

    • Official tools

      • GDC data transfert tool - Official command line tool, see [here](https://github.com/IARCbioinfo/GDC-tricks) for a nice tutorial.
      • GDC API - Official HTTP API. Note the [BAM Slicing](https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/) that can be quite useful.

    • Broad Institute GDAC

    • Others

      • GenomicDataCommons - A R/Bioconductor package for querying, accessing, and mining genomic datasets available from the GDC.
      • TCGABiolinks - A R/Bioconductor package to search, download and prepare relevant data for analysis in R. Very powerful and well documented.

  • Cloud computing

    • Others

      • Cancer Genomics Cloud - Developed by [Seven Bridges Genomics](https://www.sevenbridges.com). They have a [blog](https://www.sevenbridges.com/blog/) with useful case studies.
      • FireCloud - Developed by the BROAD Institute.
      • ISB Cancer Genomics Cloud - Developed by the Institute for Systems Biology in Seattle.

  • Pan-TCGA analyses

    • Others

      • Tumor Fusion Gene Data Portal - 9,966 tumor samples from 33 TCGA cancer types and 689 normal samples in 19 TCGA normal tissue types were analyzed by PRADA pipeline and the realigned BAM files of RNAseq data.
      • DriverDBv2 - WES and RNA-seq reanalysis to identify driver genes. Provides a nice graphical summary of mutation clustering in genes (e.g. for *[TP53](http://driverdb.tms.cmu.edu.tw/driverdbv2/gene_data_p.php?genename=TP53&geneproteinid=&submit=submit)*).
      • BioXpress - RNA-seq-derived gene expression database, including TCGA among others.
      • ASCAT Ploidy and Purity Estimates - [COSMIC](http://cancer.sanger.ac.uk/cosmic) hosts a tab separated table listing the ploidy and aberrant cell fraction (purity estimate), for TCGA samples re-analysed using ASCAT.

  • Publications

Programming Languages
R 1
Categories
Official links 9 Publications 7 Downloading the data 6 Pan-TCGA analyses 4 Cloud computing 3
Sub Categories
Others 16 Data repositories 5 General informations 4 Official tools 2 Broad Institute GDAC 2
Keywords
tcgabiolinks 1 tcga-data 1 tcga 1 r 1 integrative-analysis 1 gdc 1 bioconductor 1 bioc 1