NEWS
teal.modules.hermes 0.2.0
Enhancements
- Added
teal.logger functionality for logging changes in shiny inputs in all modules.
- Introduce
transformators parameter in modules.
teal.modules.hermes 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.
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.