NEWS

---

rWikiPathways 1.25.1

• bug fix: downloadPathwayArchive scrapes "File Name" column

rWikiPathways 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

rWikiPathways 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

rWikiPathways 1.16.0

• HTTPS updates
• Update vignette to include new clusterProfiler functions

rWikiPathways 1.14.0

• None

rWikiPathways 1.12.0

• Removed getColoredPathway
• New function: writeGMT
• Updated URLs to BridgeDb datasources.tsv (again)
• Bug fix: downloadPathwaysArchive works with redirected urls

rWikiPathways 1.11.4

• Updated URLs to BridgeDb datasources.tsv

rWikiPathways 1.11.3

• New features - new readGMT and readGMTnames methods

rWikiPathways 1.10.0

• Defuncted getColoredPathway
• Doc fix: examples fixed and sample gmt included

rWikiPathways 1.8.5

• Doc fix: added reference to clusterProfiler

rWikiPathways 1.8.4

• Doc fix: fixed Pathway Analysis vignette

rWikiPathways 1.8.3

• Bug fix: GMT parsing #16

rWikiPathways 1.8.2

• Doc fix: vignette with BridgeDbR
• Bug fix: fixed rjson replacement

rWikiPathways 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

rWikiPathways 1.6.0

• Minor updates to the Pathway Analysis vignette

rWikiPathways 1.4.1

• Bug fixes - Updated the findPathwaysByLiterature test case (fixing a false positive fail) - Removed tests for unavailable service: getColoredPathway

rWikiPathways 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

rWikiPathways 1.2.0

• Bug fixes - Added method to retrieve GMT files -- #3 issue
• Doc fixes - New vignette for pathway analysis

rWikiPathways 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!