NEWS

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• Removed outdated vignettes, now instead we point to decoupleR and decoupler-py's most up-to-date vignettes.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