Analytical Tools

 

NCI Cloud Resources are components of the NCI Cancer Research Data Commons that bring data and computational power together to enable cancer research and discovery. These cloud-based platforms eliminate the need for researchers to download and store extremely large data sets by allowing them to bring analysis tools to the data in the cloud. The platforms also provide access to on-demand computational capacity to analyze these data.

 

Selected Workflows from NCI Cloud Resources

  • VARIANT CALLING
    • SNV/indel
      • DeepVariant
      • GATK: Germline short variant discovery
    • CNV
      • Control-FREEC
      • CNVkit
      • GATK: Germline or somatic copy number variant discovery
    • Structural Variant
      • Manta
      • Novobreak
      • Delly
    • Somatic short variant calling
      • Strelka
      • VarDict
      • VarScan
      • GATK: somatic short variant discovery
  • TRANSCRIPTOMICS
    • Salmon
    • STAR
    • Kallisto
    • DESeq
    • STAR-Fusion
    • GATK: RNAseq short variant discovery
  • EPIGENOMICS
  • PROTEOMICS
    • The Trans-Proteomic Pipeline
    • x!tandem
    • (Coming soon: Philosopher)
  • IMAGING
    • TCIA archiver viewer, FSL brain segmentation
    • Machine learning with JupyterLab notebooks
      • ML/tensorflow library / GPU accelerated instances
      • CGC Docs
  • MULTI-OMICS
    • L1EM
  • SINGLE-CELL OMICS
    • Salmon-Alevin-Seurat workflow + notebook
    • Kallisto-BUS; Kallisto Psuedo
    • zUMIs
    • SmartSeq 2
    • Cumulus (Broad FireCloud only)