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Changelog

Source: NEWS.md

iSEEu 1.17.1

  • Version bump to rebuild classes derived from DotPlot.

iSEEu 1.15.1

iSEEu 1.11.2

  • Adjusted code to correctly parse and rename KEGG pathway identifiers.

iSEEu 1.11.1

  • Update ggplot2 imports for AggregatedDotPlot.

iSEEu 1.9.3

  • Fix numbering issue affecting the coloring of LogFCLogFCPlot panels.

iSEEu 1.9.2

  • Depend on the iSEEhex package to initiate the “iSEEverse”.

iSEEu 1.7.1

  • Fix bug causing .setCachedCommonInfo() to cache NULL value for valid.rowdata.names information of DynamicMarkerTable panel instead of empty character vector.

iSEEu 1.5.2

  • Fix bug causing AggregatedDotPlot to crash when a column selection was transferred.
  • Fix bug in retrieving a feature set

iSEEu 1.5.1

  • Fix spelling typo in man page.

iSEEu 1.3.5

  • Switch to registration for storing DE Panel options, via registerPValuePatterns and related functions.

iSEEu 1.3.4

  • Support in-memory feature set collections and their statistics via registerFeatureSetCollections.

iSEEu 1.3.3

  • Redistributed documentation from panel tours to UI-specific tours.

iSEEu 1.3.2

  • Tour-related patch to fix the builds for the time being.

iSEEu 1.3.1

  • Added the MarkdownBoard panel to show arbitrary Markdown-formatted content.
  • Eliminate duplicates in available fields, as these break selectizes.

iSEEu 1.1.9

  • Ensure that global parameters only affect panels during construction.

iSEEu 1.1.8

  • Added the AggregatedDotPlot panel to show marker-based dot plots.

iSEEu 1.1.7

  • Improved safety and correctness of the calculation of the number of DEGs.

iSEEu 1.1.6

  • Version bump to trigger reinstallation with new iSEE class definitions.

iSEEu 1.1.5

iSEEu 1.1.4

  • Generalized the DE-related globals to work as patterns rather directly specifying the acceptable names.
  • Align DynamicMarkerTable’s treatment of getTableExtraFields() with the globals strategy.

iSEEu 1.1.3

  • Overhauled handling of global parameters for greater consistency.
  • Added the LogFCLogFCPlot to plot two DE comparisons against each other.
  • Switched to KEGGREST to get the names of pathways.

iSEEu 1.1.2

  • Replaced GeneSetTable with the more general FeatureSetTable. Improved handling of arbitrary feature sets.
  • Renamed DifferentialStatisticsTable to the more appropriate DynamicMarkerTable. Support inclusion of extra fields from the rowData.
  • Global parameters now only affect construction of MAPlots and VolcanoPlots.

iSEEu 1.1.1

  • Improved documentation of the ReducedDimensionHexPlot methods.

iSEEu 0.99.8

  • Trigger new build on the single package builder.

iSEEu 0.99.7

  • Replace !="" by nzchar().
  • Use 4-space indent.
  • Add info on how to contribute to iSEEu, including coding style.

iSEEu 0.99.6

  • Trigger new build on the single package builder.

iSEEu 0.99.5

  • Add more suggested packages.
  • Add screenshot images to the vignette.
  • More realistic examples in the vignette.
  • Fix GeneSetTable to acknowledge initial value of "Selected".

iSEEu 0.99.4

  • Fix to GitHub action R-CMD-check.

iSEEu 0.99.3

  • Set up GitHub action R-CMD-check.
  • Remove Travis CI covr code coverage and pkgdown site deployment.
  • Fix man page warning.

iSEEu 0.99.2

  • Create observer for "Assay" in DiffStatTable.
  • Update NEWS.

iSEEu 0.99.1

  • Trigger new build on the single package builder.

iSEEu 0.99.0

  • Added panel DifferentialStatisticsTable.
  • Added panel DynamicReducedDimensionPlot.
  • Added panel GeneSetTable.
  • Added panel MAPlot.
  • Added panel ReducedDimensionHexPlot.
  • Added panel VolcanoPlot.
  • Added mode modeEmpty.
  • Added mode modeGating.
  • Added mode modeReducedDim.

iSEEu 0.1.0

  • iSEEu is officially born!