Changes in version 1.27.2 (2026-06-11)
+ Replaced remaining calls to scater::aggregateAcrossCells

Changes in version 1.27.1 (2026-06-05)
+ Replaced deprecated function scater::aggregateAcrossCells

Changes in version 1.25.1 (2026-01-28)
+ Adapted code due to changes in Seurat V5

Changes in version 1.21.1 (2024-11-07)
+ Added new functions to perform quantitative comparative pathway analyses for scRNA-seq data.

Changes in version 1.17.3 (2024-02-01)
+ Fixed a bug in vignette showcasing the reanalysis of public data.

Changes in version 1.17.2 (2023-11-28)
+ Added a set of new functions to support ReactomeGSA's features to load public datasets.
+ Added a new vignette to showcase how public datasets can easily be loaded using the ReactomeGSA package.

Changes in version 1.17.1
+ Fixed vignettes

Changes in version 1.13.1 (2023-04-13)
+ Fixed documentation mismatch in "plot_heatmap"

Changes in version 1.9.1 (2021-11-05)
+ Adapted default FDR threshold in "plot_heatmap" to match other functions.

Changes in version 1.7.5 (2021-09-28)
+ Fixed documentation of "plot_heatmap"

Changes in version 1.7.4 (2021-09-24)
+ Added new plotting function "plot_heatmap"

Changes in version 1.7.3 (2021-09-14)
+ Updated vignette to introduce the "open_reactome" command

Changes in version 1.7.2 (2021-09-09)
+ Fixed timeout issue during large requests in perform_reactome_analysis 

Changes in version 1.7.1 (2021-06-09)
+ Fixed bug in scRNA-seq vignette.

Changes in version 1.5.2 (2021-04-16)
+ Added check to ensure that clustering was performed in Seurat objects prior to the pathway analysis.

Changes in version 1.5.1 (2021-04-01)
+ Fixed bug in perform_reactome_analysis: Error messages were not displayed correctly.

Changes in version 1.3.7 (2020-09-29)
+ Fixed bug in plot_gsva_pathway

Changes in version 1.3.6 (2020-09-01)
+ Improved analyse_sc_clusters for SingleCellExperiment objects to define cell grouping using factors and a single character string specifying the metada field.

Changes in version 1.3.4 (2020-09-01)
+ Fixed bug in analyse_sc_clusters when processing SingleCellExperiment objects.

Changes in version 1.3.3 (2020-05-26)
+ Updated documentation

Changes in version 1.3.2 (2020-05-26)
+ Added workaround for SEC_E_ILLEGAL_MESSAGE error on older Windows systems.

Changes in version 1.3.1 (2020-04-29)
+ Added option to hide non-significant pathway in plot_correlations

Changes in version 1.1.4 (2020-04-20)
+ bioRxiv paper is out!

Changes in version 1.1.3 (2020-04-11)
+ Added custom function to calculate average cluster expression for Seurat objects

Changes in version 1.1.2 (2020-03-13)
+ Add support manually track the status of submitted analyses
+ Added additional signature to add_dataset to support expression values as matrix

Changes in version 1.1.1 (2020-02-19)
+ Compress JSON requests using gzip to improve performance for large datasets

Changes in version 0.99.8 (2019-08-13)
+ Removed package startup message
+ Changed spelling of name to ReactomeGSA
+ Removed all default values from the method signatures
+ Added constructor function for the ReactomeAnalysisRequest class.

Changes in version 0.99.7 (2019-07-22)
+ Adapted the get_reactome_methods function to provide a more readable overview
+ Changed to reactome analysis service API URL to the new domain name.

Changes in version 0.99.6 (2019-07-09)
+ Minor bugfixes in examples

Changes in version 0.99.5 (2019-07-09)
+ Updated vignette to new API data types
+ Added new function remove_dataset
+ Fixed bugs when overwriting existing datasets in AnalysisRequests
+ Fixed bug that pathways function did not sort the pathway table

Changes in version 0.99.0 (2019-07-01)
+ Submitted to Bioconductor
