- Added placeholders for
assaySpec
,adtteSpec
andgeneSpec
inputs when no option is selected. - Disabled the select input for
assaySpec
andadtteSpec
when there are no options available. - For module developers: The module gets
teal_data
object in the UI andreactive(<teal_data>)
in the server
- Updated the documentation and vignettes with the new way of specifying data for
teal::init()
. Thedata
argument acceptsteal_data
object. - Added
teal.logger
functionality for logging changes in shiny inputs in all modules.
- Filtering data with the filter panel now correctly triggers the
sampleVarSpecModule
.
- Replaced
datasets
argument containingFilteredData
with the new argumentsdata
(tdata
object) andfilter_panel_api
(FilterPanelAPI
).
- Removed
scda
from dependencies. - Migrate to
shinytest2
.
- Added the
teal.reporter
functionality to all modules. - Add installation instruction
- 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.
- Added a template to the
pkgdown
site. - Updated package authors.
- Added the option
categorical_only
to thesampleVarSpec
server module, which allows to only show categorical sample variables for selection.
- Rewrote modules to use
moduleServer
and updated call toplot_with_settings_srv
after changes inteal.devel
. - Replaced calls to
teal::root_modules
withteal::modules
following deprecation ofteal::root_modules
. - Added basic logging to the modules.
- Fixed the
geneSpecInput
so that thehermes
app doesn't fail anymore (on chrome) on an experiment with no genes.
- 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 thesampleVarSpecModule
.
- Updated R version requirement to >= 3.6.
- Updated
sampleVarSpec
andgeneSpec
modules with new icons to remove warnings when using shiny version >= 1.7. - Removed dependencies on deprecated packages
utils.nest
andtest.nest
.
- First release of the
teal.modules.hermes
package, which contains teal modules for RNA-seq analysis using thehermes
package. - New users should first begin by reading the
README.md
of theteal.modules.hermes
package to become familiar.
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 aKaplan-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.