NEWS

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enrichViewNet 1.9.4

BUG FIXES AND IMPROVEMENTS

• The unit tests are updated to better manager g:profiler server maintenance.
• The tests are skipped when the g:profiler server is down.

HANGES IN VERSION 1.9.3

enrichViewNet 1.9.2

NEW FEATURES

• The link to the related Code Ocean capsule has been added to the vignette.

enrichViewNet 1.9.1

BUG FIXES AND IMPROVEMENTS

• The groupCaterogy parameter has been removed from functions generating enrichment maps to follow update done in enrichplot package.

enrichViewNet 1.7.3

NEW FEATURES

• The new functions createBasicEmapAsIgraph(), createEnrichMapMultiBasicAsIgraph(), generates enrichment maps in an igraph format.

enrichViewNet 1.7.2

BUG FIXES AND IMPROVEMENTS

• All functions using ggplot2 are using updated ggplot2 functions.

enrichViewNet 1.7.1

BUG FIXES

• The package uses a fixed version of gprofiler database in the unit tests.

enrichViewNet 1.3.4

NEW FEATURES

• The 'force' parameter in createEnrichMapMultiComplex() has been removed.
• The 'force' parameter in createEnrichMapMultiBasic() has been removed.
• The 'force' parameter in createEnrichMap() has been removed.

enrichViewNet 1.3.3

NEW FEATURES

• The createEnrichMapMultiComplex() now has an new parameter ... that enables passing extra parameters to imbedded emapplot() function.
• The createEnrichMapMultiBasic() now has an new parameter ... that enables passing extra parameters to imbedded emapplot() function.
• The createEnrichMap() now has an new parameter ... that enables passing extra parameters to imbedded emapplot() function.

enrichViewNet 1.3.2

BUG FIXES

• The package uses the Ensembl list rather than the query list to extract information when intersection column is missing, in the extractInformationWhenNoIntersection() function.

enrichViewNet 1.3.1

BUG FIXES

• The package uses the information about the organism when querying the gprofiler database.

enrichViewNet 1.1.2

NEW FEATURES

• The new function createEnrichMapMultiBasic() enables the creation of enrichment maps with groups from simple designs.
• The new function createEnrichMapMultiComplex() enables the creation of enrichment maps with groups from complex designs.

SIGNIFICANT USER-VISIBLE CHANGE

• The vignette contains new sections presenting the new functions createEnrichMapMultiBasic() and createEnrichMapMultiComplex().

enrichViewNet 1.1.1

SIGNIFICANT USER-VISIBLE CHANGE

• The enrichViewNet workflow figure, in the vignette, has been updated.

enrichViewNet 0.99.2

NEW FEATURES

• The man pages are respecting 80 character width.

enrichViewNet 0.99.1

NEW FEATURES

• The 'Installation' and 'Introduction' sections of the vignette have been updated.

enrichViewNet 0.99.0

NEW FEATURES

• The new createEnrichMap() function enables the creation of an enrichment map from enrichment results.

enrichViewNet 0.0.4

NEW FEATURES

• When 'intersection' column present in the GOST object, the software uses the column to create the output for Cytoscape, without having to call gconvert() function. The output is generated much more rapidly.

enrichViewNet 0.0.2

NEW FEATURES

• Added a NEWS.md file to track changes to the package.

SIGNIFICANT USER-VISIBLE CHANGES

• The createNetwork() method has a new parameter 'fileName' that enables the creation of a CX JSON file when Cytoscape is not running.

BUG FIXES

• The createCytoscapeCXJSON() method does not replicate anymore the genes that are associated to more than one term.