Changes in version 1.1.2                        

  - Fix bug where DEXSeq fails if there are NAs in the metadata

                        Changes in version 1.1.1                        

  - Improved how surrogate variables are transferred in the design
    formulas

                        Changes in version 1.1.0                        

  - paired_ora now adjusts gene background for analysis to reduce bias
  - paired_ora now also does an ora combining the genes from the two
    analyses
  - Added plotting mode paired = TRUE to plot_ora for the new paired_ora
    analysis type
  - Added baseMean to gene-level aggregation output

                        Changes in version 1.0.0                        

  - Version bump for Bioconductor release
  - Minor edits to documentation

                       Changes in version 0.99.6                        

  - Improved test coverage and depth
  - Coerced paired_ora output to DataFrame from data.table
  - Added value field to data man pages

                       Changes in version 0.99.5                        

  - Remove non-exported man pages

                       Changes in version 0.99.4                        

  - Remove filter_gene_sets option, as it is inherent in fgsea::ora
  - Added test depth and coverage for paired_diff and paired_ora
  - Fixed wrong storing location for splicing intermediate results

                       Changes in version 0.99.3                        

  - Rewrote code base to remove tidyverse dependencies
  - Added \code{...} and \link{...} where appropriate in documentation
  - Added input parameter checks
  - Reduced redundant input parameters from aggregate_pvalue
  - Modularized paired_ora and plot_ora
  - Added filter_gene_sets parameter to help users reduce gene set bias
  - Increased test coverage and depth
  - Moved data scripts to inst/script

                       Changes in version 0.99.2                        

  - Implement limma as alternative analysis method
  - Increased test coverage significantly
  - Removed usage of deprecated purrr::when

                       Changes in version 0.99.1                        

  - Updated vignette with a brief paragraph on the motivation of
    pairedGSEA.
  - Updated NAMESPACE to include all imported packages. Suggested
    packages are added in notes.

                       Changes in version 0.99.0                        

  - Submitted to Bioconductor