v0.1.6

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.

What's Changed

• Workflow propagation by @walkowif in #328
• Use token in spelling workflow by @walkowif in #329
• Disable dropdown on encondings if no option is available by @averissimo in #332
• Only retain hard dependencies from pre-commit hooks by @averissimo in #333
• 330 Fix integration test (update adtteSpec snapshott) by @BFalquet in #334
• 198 Include user's card labels when generating the report by @kartikeyakirar in #336
• 339 migrate to teal data@main by @m7pr in #342
• add teal.data in package imports by @donyunardi in #347
• Using teal_data in the modules instead of tdata by @vedhav in #344
• Workflow propagation by @walkowif in #350
• silent logger in tests by @pawelru in #353
• Fix pkgdown redirect by @vedhav in #356
• Fix broken examples by @vedhav in #351
• 355: Add load_timeout = 30000 to AppDriver::new() calls by @danielinteractive in #357
• new release by @danielinteractive in #358

New Contributors

• @averissimo made their first contribution in #332
• @kartikeyakirar made their first contribution in #336

Full Changelog: v0.1.5...v0.1.6

v0.1.5

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.

What's Changed

• [skip vbump] Dev version with 9xxx by @arkadiuszbeer in #292
• 282 Migrate to shinytest2 by @BFalquet in #286
• Add coverage badge by @walkowif in #296
• updates from issue 61 by @sob2021 in #295
• Teal refactor by @nikolas-burkoff in #294
• Enable checks for workflow_dispatch event by @walkowif in #297
• Badges and contribution guidelines by @insights-engineering-bot in #298
• 251 Add a getting started vignette by @BFalquet in #300
• Update check as-cran and default landing page by @walkowif in #301
• Update rtables staged dep by @edelarua in #304
• adding rmarkdown to suggests by @arkadiuszbeer in #305
• Update token name by @walkowif in #306
• Add NOT_CRAN=true to run shinytest2 tests by @cicdguy in #302
• Update workflows by @walkowif in #308
• Workflow propagations by @walkowif in #309
• reduce the amount of spelling issues / WORDLIST by @m7pr in #310
• 311 decouple scda by @m7pr in #312
• fix filter-panel namespace ids by @gogonzo in #314
• update installation instruction by @gogonzo in #316
• propagate argument name change in teal::module by @chlebowa in #317
• 323 [Bug]: Uncaught error in Barplot module by @BFalquet in #326
• release 0.1.5 [skip vbump] [skip spelling] by @donyunardi in #327

New Contributors

• @walkowif made their first contribution in #296
• @sob2021 made their first contribution in #295
• @edelarua made their first contribution in #304
• @m7pr made their first contribution in #310
• @chlebowa made their first contribution in #317
• @donyunardi made their first contribution in #327

Full Changelog: v0.1.4...v0.1.5

v0.1.4

• 0.1.4

What's Changed

• fix news by @gogonzo in #259
• Contribution guide updates by @insights-engineering-bot in #260
• docs: replaced github links with pkgdown by @kpagacz in #261
• readme and desc by @denisovan31415 in #262
• Update Rbuildignore and add auto-updates by @insights-engineering-bot in #263
• Add reporter by @mhallal1 in #265
• add reporter to remotes by @nikolas-burkoff in #268
• Update pre-commit config to detect _pkgdown.y[a]ml by @insights-engineering-bot in #269
• reporter cleaning by @mhallal1 in #270
• Update documentation workflow by @insights-engineering-bot in #273
• tmh css by @Polkas in #272
• Merge pre-release to main by @cicdguy in #276
• Update check.yaml by @arkadiuszbeer in #277
• Renamed drop-down to Select Categorical Subgroup Variable. by @AniaGolab in #283
• Removing if condition for by @arkadiuszbeer in #280
• Fix reporting issues by @nikolas-burkoff in #285
• 287: adjust error capture by @danielinteractive in #288
• 289: make missing levels of sample variables optionally explicit by @danielinteractive in #290
• [skip vbump] Release for version 0.1.4 by @insights-engineering-bot in #291

New Contributors

• @AniaGolab made their first contribution in #283

Full Changelog: v0.1.3...v0.1.4

v0.1.3

• 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.

v0.1.1

Bug Fixes

• 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.

v0.1.0

• 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.