Changes in version 0.2.0                        

Enhancements

  - Added teal.logger functionality for logging changes in shiny inputs
    in all modules.
  - Introduce transformators parameter in modules.

                     Changes in version 0.1.6.9033                      

Miscellaneous

  - Added placeholders for assaySpec, adtteSpec and geneSpec inputs when
    no option is selected.
  - Disabled the select input for assaySpec and adtteSpec when there are
    no options available.
  - For module developers: The module gets teal_data object in the UI
    and reactive(<teal_data>) in the server

Enhancements

  - Updated the documentation and vignettes with the new way of
    specifying data for teal::init(). The data argument accepts
    teal_data object.

                        Changes in version 0.1.5                        

Bug Fixes

  - Filtering data with the filter panel now correctly triggers the
    sampleVarSpecModule.

Breaking changes

  - Replaced datasets argument containing FilteredData with the new
    arguments data (tdata object) and filter_panel_api (FilterPanelAPI).

Miscellaneous

  - Removed scda from dependencies.
  - Migrate to shinytest2.

                        Changes in version 0.1.4                        

  - Added the teal.reporter functionality to all modules.
  - Add installation instruction

                        Changes in version 0.1.3                        

  - Improve the selection of sample variables in the forest module
    (tm_g_forest_tte) such that only categorical variables can be
    selected in the first place.

Miscellaneous

  - Added a template to the pkgdown site.
  - Updated package authors.
  - Added the option categorical_only to the sampleVarSpec server
    module, which allows to only show categorical sample variables for
    selection.

                        Changes in version 0.1.2                        

  - Rewrote modules to use moduleServer and updated call to
    plot_with_settings_srv after changes in teal.devel.
  - Replaced calls to teal::root_modules with teal::modules following
    deprecation of teal::root_modules.
  - Added basic logging to the modules.
  - Fixed the geneSpecInput so that the hermes app doesn't fail anymore
    (on chrome) on an experiment with no genes.

                        Changes in version 0.1.1                        

Bug Fixes

  - Updated legend for the PCA plot.
  - Gene selection with more than a few thousand genes no longer hangs
    the application. This is achieved through a different selection
    input in the corresponding geneSpec shiny module.
  - Only atomic columns of colData with at least one value can now be
    selected in the sampleVarSpecModule.

Miscellaneous

  - Updated R version requirement to >= 3.6.
  - Updated sampleVarSpec and geneSpec modules with new icons to remove
    warnings when using shiny version >= 1.7.
  - Removed dependencies on deprecated packages utils.nest and
    test.nest.

                        Changes in version 0.1.0                        

  - First release of the teal.modules.hermes package, which contains
    teal modules for RNA-seq analysis using the hermes package.
  - New users should first begin by reading the README.md of the
    teal.modules.hermes package to become familiar.

New Features

  - tm_g_barplot is a barplot module for RNA-seq gene expression
    analysis.
  - tm_g_boxplot is a boxplot module for RNA-seq gene expression
    analysis.
  - tm_g_forest_tte is a survival forest plot module to analyze RNA-seq
    gene expression data together with survival data.
  - tm_g_km is a Kaplan-Meier plot module to analyze RNA-seq gene
    expression data together with survival data.
  - tm_g_pca is a principal components analysis plot module for RNA-seq
    gene expression analysis.
  - tm_g_quality is a quality control module for RNA-seq gene expression
    data.
  - tm_g_scatterplot is a scatterplot module for RNA-seq gene expression
    analysis.
  - tm_g_volcanoplot is a differential gene expression analysis module.