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  • Source Data
    • Types of Data
    • Sources
    • Metadata
      • refine.bio-harmonized Metadata
      • Submitter Supplied Metadata
  • Processing Information
    • refine.bio processed
      • Microarray pipelines
        • Affymetrix
        • Illumina BeadArrays
      • RNA-seq pipelines
        • Salmon
        • tximport
    • Submitter processed
      • Affymetrix identifier conversion
      • Illumina identifier conversion
    • Aggregations
      • Limitations of gene identifiers when combining across platforms
    • Transformations
      • Quantile normalization
        • Reference distribution
        • Quantile normalizing samples for delivery
        • Limitations of quantile normalization across platforms with many zeroes
        • Skipping quantile normalization for RNA-seq experiments
      • Gene transformations
  • Downloadable Files
    • The download folder structure for data aggregated by experiment:
    • The download folder structure for data aggregated by species:
    • Gene Expression Matrix
    • Sample Metadata
      • TSV files
      • JSON files
    • Experiment Metadata
  • refine.bio Compendia
    • Normalized compendia
      • Collapsing by genus
      • Normalized Compendium Download Folder
    • RNA-Seq Sample Compendia
      • RNA-Seq Sample Compendium Download Folder
  • API
  • Downstream Analysis with refine.bio Examples
  • Getting Started with a refine.bio dataset
    • Structure
    • Contents
    • Usage
      • Reading TSV Files
      • Reading JSON Files
  • Getting Started with Normalized Compendia
    • Structure
    • Contents
    • Notes and observations
      • Methods evaluation and exploratory data analysis
    • Usage
      • Reading TSV Files
      • Reading JSON Files
  • FAQ
    • What is the difference between refine.bio-processed and submitter-processed datasets?
    • How do you process the data?
    • What type of data does refine.bio support?
    • What does “corrected” metadata mean?
    • Why do the values differ a little bit if I download different datasets?
    • Why do I get a limited number of genes back when I aggregate samples from different experiments?
    • Why can’t I add certain samples to my dataset?
    • Why do the genes included in RNA-seq experiments change between experiments from the same organism?
    • How can I find out what genome build and release were used to process RNA-seq data?
    • How can I find out what versions of software/packages were used to process the data?
    • Are refine.bio datasets I download batch corrected?
    • Why are the expression values different if I regenerate a dataset?
    • What does it mean to skip quantile normalization for RNA-seq samples?
    • How do I cite refine.bio?
  • License
refine.bio
  • Search

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