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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
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