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dorothea 1.7.3 (2023-04-21)

  • Added CollecTRI and deprecated run_viper function for decoupleR.

dorothea 1.7.1 (2022-04-07)

  • Removed outdated vignettes, now instead we point to decoupleR and decoupler-py's most up-to-date vignettes.

dorothea 1.5.2 (2021-10-13)

  • Daniel Dimitrov is assigned as the new maintainer

dorothea 1.4.2 (2021-10-08)

  • Fixed lazy data warning
  • Improved test coverage

dorothea 1.4.1 (2021-05-25)

  • Rebuild all regulons
  • Fixed ambiguously mode of regulation in mouse regulons

dorothea 1.3.2 (2021-03-09)

  • Added pancancer regulons for application in cancer.

dorothea 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.

dorothea 1.1.3 (2020-10-26)

  • Fixed bug in single-cell vignette

dorothea 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.

dorothea 1.1.1 (2020-09-02)

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

dorothea 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

dorothea 1.0.0 (2020-04-27)

  • Official release in Bioconductor 3.11

dorothea 0.99.9 (2020-04-22)

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

dorothea 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

dorothea 0.99.0 (2020-04-03)

  • Initial submission to Bioconductor