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