Changes in version 1.7.3 (2023-04-21) - Added CollecTRI and deprecated run_viper function for decoupleR. Changes in version 1.7.1 (2022-04-07) - Removed outdated vignettes, now instead we point to decoupleR and decoupler-py's most up-to-date vignettes. Changes in version 1.5.2 (2021-10-13) - Daniel Dimitrov is assigned as the new maintainer Changes in version 1.4.2 (2021-10-08) - Fixed lazy data warning - Improved test coverage Changes in version 1.4.1 (2021-05-25) - Rebuild all regulons - Fixed ambiguously mode of regulation in mouse regulons Changes in version 1.3.2 (2021-03-09) - Added pancancer regulons for application in cancer. Changes in version 1.2.1 (2021-02-08) - Fixed bug in Seurat's related unit tests due to Seurats package update to version 4.0. s@assays$dorothea@misc is now list(), before it was NULL. Changes in version 1.1.3 (2020-10-26) - Fixed bug in single-cell vignette Changes in version 1.1.2 (2020-10-08) - Changed TF census from TFclass to the more recent version from Lambert et al.. Information of mode of regulation for each TF (activator, supressor, dual) is still taken from Garcia-Alonso et al.. - Updated gene symbols to their latest alias with the limma package (version 3.44.3). - Shifted viper package from suggest to depends in the DESCRIPTION file. - Added a further argument specifially for run_viper.Seurat() to select a specific assay name to extract the normalized gene expression values from. Changes in version 1.1.1 (2020-09-02) - Export df2regulon() function - Improved documentation (added gh page URL to DESCRIPTION) Changes in version 1.0.1 (2020-08-13) - Improved package documentation - Updated link to 10x genomics data set in single-cell vignette - Fixed tests related to Seurat and SCE class Changes in version 1.0.0 (2020-04-27) - Official release in Bioconductor 3.11 Changes in version 0.99.9 (2020-04-22) - Integration of Travis CI - Integrated unit test coverage with covr::codecov - Build github page via pkgdown Changes in version 0.99.1 (2020-04-06) - If the input to the viper wrapper is a Bioconductor class, this Bioconductor class is retured with added TF activities at appropiate slots - Expanded the viper wrapper to the Bioconductor class SingleCellExperiment Changes in version 0.99.0 (2020-04-03) - Initial submission to Bioconductor