- Parameters for all data types
- study-params.md - Parameters that are supported for all data types.
- Metadata
- tags.md - Loading study, concept, patient metadata and links to source data per concept.
- 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.
- 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.
- General high-dimensional data processing
- hd-params.md - Parameters that are supported for all high-dimensional data types.
- chromosomal_region.md - Tabular file structure for loading chromosomal regions.
- subject-sample-mapping.md - Tabular file structure for loading subject sample mappings for HD data.
- 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
- metabolomics.md - Loading metabolite quantities.
- GWAS data
- gwas.md - Loading Genome Wide Association Study data.
- Unloading tranSMART data
- backout.md - Deleting data from tranSMART.
- Loading I2B2 data
- i2b2.md - Loading data to I2B2 with transmart-batch.