NEWS

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pairedGSEA 1.1.2

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

pairedGSEA 1.1.1

• Improved how surrogate variables are transferred in the design formulas

pairedGSEA 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

pairedGSEA 1.0.0

• Version bump for Bioconductor release
• Minor edits to documentation

pairedGSEA 0.99.6

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

pairedGSEA 0.99.5

• Remove non-exported man pages

pairedGSEA 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

pairedGSEA 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

pairedGSEA 0.99.2

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

pairedGSEA 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.

pairedGSEA 0.99.0

• Submitted to Bioconductor