NEWS

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pathlinkR 1.1.22

• Expanded and clarified error messages for pathwayEnrichment input
• Updated vignette

pathlinkR 1.1.18

• Fixed bug for pathwayEnrichment when running fgsea (NA gene names)

pathlinkR 1.1.17

• Fix for default parameters and theme settings in ppiPlotNetwork
• Support for GSEA (via package fgsea), both as an option in pathwayPlots and pathwayEnrichment
• Global fontSize argument added to pathwayPlots

pathlinkR 1.1.10

• Support for KEGG pathways when running pathwayEnrichment, either through Sigora or traditional over-representation

pathlinkR 1.1.8

• pathwayPlots now supports the output from fgsea on Reactome pathways (109a173)

pathlinkR 1.1.7

• Size of asterisks in pathwayPlots is set based on tringle size (1f9b751)

pathlinkR 1.1.6

• Updated installation information in README
• "eruption" gained argument "labelCutoffs" to add labels to p value and fold change cutoff lines
• "ppiPlotNetwork" checks for argument "labelColumn" when "label=TRUE"
• Fixed some tests

pathlinkR 0.99.380

Lots of updates, including:

• Updated documentation for data and functions
• Cleaner vignette
• Better support for Bioconductor classes
• Better handling of data loading

pathlinkR 0.99.352

• Added value tag to data documentation

pathlinkR 0.99.350

• Rewrite of pathwayPlots to be more efficient

pathlinkR 0.99.332

• Changed methodology for importing functions
• Added two new functions for PPI networks: "ppiEnrichNetwork" and "ppiExtractSubnetwork"

pathlinkR 0.99.317

• Renamed a number of functions to improve consistency, and make it clear which ones are related and part of the same "workflow"

pathlinkR 0.99.310

• Big update to the vignette
• Update to the README and added in the package hex logo
• Various function tweaks and minor changes

pathlinkR 0.99.300

• Renamed package to pathlinkR

pathlinkR 0.99.1

• Prepared for bioconductor submission