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Awesome

An open API service indexing awesome lists of open source software.

awesome-TCGA

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

Last synced: 1 day ago
JSON representation

    • General informations

      • 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.
      • 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

      • Python and UNIX wrappers
      • Firebrowse - A web UI to visualise the results of the analyses performed by Firehose.
      • Firebrowse - A web UI to visualise the results of the analyses performed by Firehose.
      • FirebrowseR - An R package to download directly the results of the analyses performed by Firehose in R.

    • Others

      • GenomicDataCommons - A R/Bioconductor package for querying, accessing, and mining genomic datasets available from the GDC.
      • gdctools - Broad Institute Python and UNIX CLI utilities to simplify search and retrieval of open-access data from the GDC.
      • GDC Spreadsheet Download Tool - Tool to download clinical and/or biospecimen metadata for a given set of files in a tab-delimited format.

  • 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.
      • 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.
      • 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)*).

  • Publications

Programming Languages
Python 1
Categories
Official links 10 Downloading the data 9 Publications 8 Pan-TCGA analyses 5 Cloud computing 3
Sub Categories
Others 19 Data repositories 5 General informations 5 Broad Institute GDAC 4 Official tools 2