Changelog • dorothea

Added CollecTRI and deprecated run_viper function for decoupleR.

Removed outdated vignettes, now instead we point to decoupleR and decoupler-py’s most up-to-date vignettes.

Daniel Dimitrov is assigned as the new maintainer

Fixed lazy data warning
Improved test coverage

Rebuild all regulons
Fixed ambiguously mode of regulation in mouse regulons

Added pancancer regulons for application in cancer.

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.

Fixed bug in single-cell vignette

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.

Export df2regulon() function
Improved documentation (added gh page URL to DESCRIPTION)

Improved package documentation
Updated link to 10x genomics data set in single-cell vignette
Fixed tests related to Seurat and SCE class

Official release in Bioconductor 3.11

Integration of Travis CI
Integrated unit test coverage with covr::codecov
Build github page via pkgdown

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

Initial submission to Bioconductor