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Exploring refine.bio species compendia

Once refine.bio reaches production, we will periodically release compendia comprised of all the samples from a species that we were able to process. We refer to these as species compendia and envision that these collections will be useful for extracting features from a diverse set of biological conditions. Creating a species compendia pipeline required us to tackle various problems such as selecting a method for imputing missing values. This repository holds a series of analyses related to refine.bio species compendia divided up into related modules. See the README files in the individual directories for more information.

Modules

  • select_imputation_method - A series of experiments/evaluations for selecting a method for imputing missing values.
  • human_missingness - Typically genes that are measured in less than 30% of samples are removed before imputing missing values in gene expression data. How many genes would be left in the human compendium using this cutoff?
  • impute_requirements - How long does it take to run KNN impute? (Too long for our use case.)
  • quality_check - Exploring test zebrafish compendia.

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A series of analyses related to refine.bio species compendia

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