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‼️ THIS WIKI IS NO LONGER MAINTAINED - PLEASE REFER TO THE VIGNETTE INSTEAD ‼️

Welcome to the BASiCS wiki!

This wiki provides documentation that complements the BASiCS vignette. Subpages provide easily accessible information regarding particular features of the BASiCS package. Please contact us if you find any issues or have any suggestions.

Prior to the Bioconductor release of BASiCS, several functions have changed with respect to our original release. We aimed to minimise these changes, implementing only those that improve the functionality of the library. A summary of the main changes is provided below:

• Data class. The BASiCS_Data class has been removed and replaced by the SingleCellExperiment class. This provides easier interaction with other Bioconductor packages that are based on this newly created data class.

• BASiCS_Chain and BASiCS_Summary classes. The definition of these classes has been updated to allow more flexibility and accommodate ongoing extensions. All parameters are now stored as a list into a single parameters slot.

  • If you used BASiCS before its release in Bioconductor: the BASiCS_LoadChain function has been updated to convert old BASiCS_Chain object to be compatible with the new class definition. Use StoreUpdatedChain = TRUE to store the updated BASiCS_Chain object as a single .Rds (this overwrites the original input .Rds file).

• MCMC chain storage. If requested, the output of the BASiCS_MCMC function is now stored as a single .Rds file (as opposed to multiple .txt files).

  • If you used BASiCS before its release in Bioconductor: the BASiCS_LoadChain function has been updated to be compatible with both storage formats. Use StoreUpdatedChain = TRUE to store the BASiCS_Chain object as a single .Rds.

• HVG/LVG detection. A new rule has been implemented to choose a posterior probability threshold. This is defined by setting the EFDR to a user-defined value.

• Differential tests. Several changes have been implemented in the BASiCS_TestDE function (this replaces BASiCS_D_TestDE):

  • Log-fold changes are now defined in a log2 scale.
  • Enhanced plots are provided to summarise the offset effect and the results of the differential test.
  • Separate tables are provided to summarise the results of the differential mean and over-dispersion tests.
  • The differential over-dispersion test excludes those genes detected by the differential mean test.