Changes in version 1.29.1 o README: cite latest WikiPathways paper o README: updated a few links (including a relative link) o README: removed a link to an unmaintained file o removed .travis.yml Changes in version 1.28.0 o None Changes in version 1.25.1 o bug fix: downloadPathwayArchive scrapes "File Name" column Changes in version 1.22.0 o Reimplementation of every function, replacing web service with static JSON o getRecentChanges now returns data.frame of pathways per last-edit date o findPathwaysByText has new param, "field" to optionally specify which fields to search o getPathwayHistory now opens pathway commit history in browser o getPathwayInfo now returns all pathways if param is left NULL o New functions: - listCommunities - getPathwaysByCommunity - getPathwayXXXsByCommunity - getCounts - findPathwaysByOrcid - getCurationStatus o Deprecated functions: - getCurationTags - getCurationTagNames - getXXXByCurationTag - wikipathwaysAPI - wikipathwaysGET Changes in version 1.17.1 o doc fix: dplyr redundant, throws error o doc fix: specify rjson and lib packages in Rmd o README: removed Travis-CI badge (discontinued) o README: added latest WikiPathways paper Changes in version 1.16.0 o HTTPS updates o Update vignette to include new clusterProfiler functions Changes in version 1.14.0 o None Changes in version 1.12.0 o Removed getColoredPathway o New function: writeGMT o Updated URLs to BridgeDb datasources.tsv (again) o Bug fix: downloadPathwaysArchive works with redirected urls Changes in version 1.11.4 o Updated URLs to BridgeDb datasources.tsv Changes in version 1.11.3 o New features - new readGMT and readGMTnames methods Changes in version 1.10.0 o Defuncted getColoredPathway o Doc fix: examples fixed and sample gmt included Changes in version 1.8.5 o Doc fix: added reference to clusterProfiler Changes in version 1.8.4 o Doc fix: fixed Pathway Analysis vignette Changes in version 1.8.3 o Bug fix: GMT parsing #16 Changes in version 1.8.2 o Doc fix: vignette with BridgeDbR o Bug fix: fixed rjson replacement Changes in version 1.8.0 o Replaced RJSONIO with rjson o Replaced all but one sapply() with vapply() o Deprecated getColoredPathway o New features - Upgraded findPathwaysByXXX, listPathways and getPathwayInfo functions to return dataframes - Upgraded findPathwaysByLiterature to present literature fields o Doc fixes - Updated tests and vignettes using dataframes Changes in version 1.6.0 o Minor updates to the Pathway Analysis vignette Changes in version 1.4.1 o Bug fixes - Updated the findPathwaysByLiterature test case (fixing a false positive fail) - Removed tests for unavailable service: getColoredPathway Changes in version 1.4.0 o Bug fixes - Added XML to Imports -- #4 missing import o 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 o Bug fixes - Added method to retrieve GMT files -- #3 issue o Doc fixes - New vignette for pathway analysis Changes in version 1.0.0 o 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 o 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!