Changes in version 1.22.0 + Reimplementation of every function, replacing web service with static JSON + getRecentChanges now returns data.frame of pathways per last-edit date + findPathwaysByText has new param, "field" to optionally specify which fields to search + getPathwayHistory now opens pathway commit history in browser + getPathwayInfo now returns all pathways if param is left NULL + New functions: - listCommunities - getPathwaysByCommunity - getPathwayXXXsByCommunity - getCounts - findPathwaysByOrcid - getCurationStatus + Deprecated functions: - getCurationTags - getCurationTagNames - getXXXByCurationTag - wikipathwaysAPI - wikipathwaysGET Changes in version 1.17.1 + doc fix: dplyr redundant, throws error + doc fix: specify rjson and lib packages in Rmd + README: removed Travis-CI badge (discontinued) + README: added latest WikiPathways paper Changes in version 1.16.0 + HTTPS updates + Update vignette to include new clusterProfiler functions Changes in version 1.14.0 + None Changes in version 1.12.0 + Removed getColoredPathway + New function: writeGMT + Updated URLs to BridgeDb datasources.tsv (again) + Bug fix: downloadPathwaysArchive works with redirected urls Changes in version 1.11.4 + Updated URLs to BridgeDb datasources.tsv Changes in version 1.11.3 + New features - new readGMT and readGMTnames methods Changes in version 1.10.0 + Defuncted getColoredPathway + Doc fix: examples fixed and sample gmt included Changes in version 1.8.5 + Doc fix: added reference to clusterProfiler Changes in version 1.8.4 + Doc fix: fixed Pathway Analysis vignette Changes in version 1.8.3 + Bug fix: GMT parsing #16 Changes in version 1.8.2 + Doc fix: vignette with BridgeDbR + Bug fix: fixed rjson replacement Changes in version 1.8.0 + Replaced RJSONIO with rjson + Replaced all but one sapply() with vapply() + Deprecated getColoredPathway + New features - Upgraded findPathwaysByXXX, listPathways and getPathwayInfo functions to return dataframes - Upgraded findPathwaysByLiterature to present literature fields + Doc fixes - Updated tests and vignettes using dataframes Changes in version 1.6.0 + Minor updates to the Pathway Analysis vignette Changes in version 1.4.1 + Bug fixes - Updated the findPathwaysByLiterature test case (fixing a false positive fail) - Removed tests for unavailable service: getColoredPathway Changes in version 1.4.0 + Bug fixes - Added XML to Imports -- #4 missing import + Doc fixes - Fixed sign in subsetting function in vignette -- user issue on bioc forum - Added the missing References section to one of the vignettes - Added BioSchemas annotation to the vignettes Changes in version 1.2.0 + Bug fixes - Added method to retrieve GMT files -- #3 issue + Doc fixes - New vignette for pathway analysis Changes in version 1.0.0 + New features - Added derivative functions for both listPathways and getPathwaysByXref to allow specifying the return of simple lists of WPIDs, URLs or names. - Added support for PNG from getColoredPathway - Added functions for all remaining web service API methods - Added a download function for archived pathway sets in various formats - Added Overview and BridgeDbR vignettes + Significant changes under the hood - Updated all functions to use REST calls instead of Curl - Simplified function development by abstracting as dedicated wikipathwaysGET function - Added tests for all new functions - Added enumerated parameters in a number of places for better input validation +Bug fixes - First official release. No bugs... yet!