NEWS

iCOBRA 1.31.2

Added 'Close app' button to close the shiny app

iCOBRA 1.5.5

The default selection of the measure to use for ROC and FP curves have been changed to improve consistency. Now, the preferred order is pval, padj, score. The behaviour of previous versions can be obtained by setting prefer_pval = FALSE in calculate_performance(). Note that the type of measure that is used to calculate a certain performance value can be retrieved from the respective slots of the COBRAPerformance and COBRAPlot objects.
Improved robustness in selection of measure to use for FDR/TPR and FDR/NBR curves, especially for methods where both p-values and scores are available.
Additional validity checks for pval and padj slots

iCOBRA 1.5.1

Added support for false sign rate calculations

iCOBRA 0.99.10

Fixed the call to plot_upset to avoid duplicate definition of arguments

iCOBRA 0.99.9

Added CITATION file, extended some examples

iCOBRA 0.99.8

Include UpSet plots (Lex et al, IEEE Transactions on Visualization and Computer Graphics 2014)

iCOBRA 0.99.7

Allow linewidth to be set, add Venn diagrams based on rank cutoffs

iCOBRA 0.99.5

Updated documentation

iCOBRA 0.99.4

Expanded tests, added experimental function to reorder factor levels before plotting

iCOBRA 0.99.3

Bug fixes

iCOBRA 0.99.2

Fixed replacement methods for COBRAPlot class

iCOBRA 0.99.1

Removed benchmarkR dependence

iCOBRA 0.3.13

Adapted package for Bioconductor submission

iCOBRA 0.3.11

Renamed to iCOBRA

iCOBRA 0.3.9

Improved constructors

iCOBRA 0.3.8

Added check for duplicated feature IDs

iCOBRA 0.3.7

Fixed bug causing problems for Venn diagrams if only one method is available
Included information texts in app

iCOBRA 0.3.5

Simplified constructors

iCOBRA 0.3.4

Modified calculation of overlaps

iCOBRA 0.3.2

Added unit tests

iCOBRA 0.3.1

Updated information messages in app

iCOBRA 0.3.0

Bug fixes in app
Addition of small example data set
Addition of information banners to app

iCOBRA 0.2.0

Added deviation plot
Bug fixes