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Changelog

Source: NEWS.md

teal.modules.hermes 0.1.6

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.

teal.modules.hermes 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.

teal.modules.hermes 0.1.4

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

teal.modules.hermes 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.

teal.modules.hermes 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.

teal.modules.hermes 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.

teal.modules.hermes 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.