NEWS.md

In csoneson/iSEEu: iSEE Universe

iSEEu 1.17.1

• Version bump to rebuild classes derived from DotPlot.

iSEEu 1.15.1

• Expanded the content of the vignette, to have AggregatedDotPlot() and the MarkdownBoard() panels highlighted

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

• Added panel-specific tours for all panel classes via the .definePanelTour() generic.

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!

csoneson/iSEEu documentation built on Oct. 16, 2024, 4:50 a.m.