Skip to content

Latest commit

 

History

History
 
 

data_formats

Loading tranSMART data

For all data types

  • Parameters for all data types
  • Metadata
    • tags.md - Loading study, concept, patient metadata and links to source data per concept.

Low-dimensional data

  • Clinical data
    • clinical.md - Loading numerical and categorical low-dimensional data from clinical, non-high throughput molecular profiling, derived imaging data, biobanking data or links to source data per patient.
      • templates.md - Using templates in the clinical data paths.
      • xtrial.md - Uploading across trial clinical data.

High-dimensional data

  • General high-dimensional data processing
  • mRNA gene expression data
    • expression.md - Loading microarray gene expression data.
    • under development - Loading readcounts and normalized readcounts data for mRNAseq and miRNAseq.
  • Copy Number Variation data
    • cnv.md - Loading CNV data from Array CGH (comparative genomic hybridisation), SNP Array, DNA-Seq, etc.
  • Small Genomic Variants
    • not yet implemented - Loading small genomic variants (SNP, indel in VCF format) from RNAseq or DNAseq.
  • Proteomics data
    • proteomics.md - Loading protein mass spectrometry data as peptide or protein quantities.
  • RnaSeq data
    • rnaseq.md - Loading gene region RNASeq data as read counts and normalized read counts.
  • Metabolomics data
  • GWAS data
    • gwas.md - Loading Genome Wide Association Study data.

Other

  • Unloading tranSMART data
  • Loading I2B2 data
    • i2b2.md - Loading data to I2B2 with transmart-batch.