v3.0

Major changes

• Parameter names changed to be more consistent between functions and to follow a common nomenclature.
• New data sources
  • PFCOR v20240901 (2024-09-28)
  • Rhea Release 134 (2024-07-24)
  • RefMet v20250305 (2025-03-05)
• Updates from previous data sources
  • Reactome v89 (2024-06)
  • WikiPathways v20240810 (2024-08-10)
  • ChEBI Release 236 (2024-07-27)
  • LIPID MAPS Release (2024-08-19)
• Code updates to use sqlite rather than mysql database
• New functions focused on reactions
  • getReactionClassesForAnalytes()
  • getReactionsForAnalytes()
• Additional enrichment functions added
  • runEnrichOntologies()
  • runEnrichReactionClass()
• New functions for visualizations
  • plotChemicalClass() - interactive
  • plotReactionClasses() - interactive
  • plotAnalyteOverlapPerRxnLevel() - interactive
  • plotOntologyEnrichmentResults()
• Updated vignette

Additional Details

• refactor: add RaMP class and utilities to download dbs by @jorainer in #57
• dockerize the travis config, and run the RaMP unit tests by @KeithKelleher in #66
• patch rxn stats code, add pathway filters to getPathwayFromAnalyte by @johnbraisted in #70
• Mysql unit tests by @KeithKelleher in #72
• Reaction Plots (sunburst and upset) added in by @mehtaky in #73
• update bioconductor link for travis' test script by @KeithKelleher in #75
• Merge sqlite branch into main by @johnbraisted in #78
• update to README.md by @johnbraisted in #79
• remove mysql tests because mysql is going away anyway by @KeithKelleher in #77
• Merge pull request #79 from ncats/sqlite by @KeithKelleher in #80
• updates to travis unit tests by @KeithKelleher in #81
• Fixed the warnings from check() by @Mathelab in #85
• Fixed remaining warnings and vignette works. by @Mathelab in #86
• 2 fixes - case sensitive duplicate names in getOntoFromMeta, and joining common names with a pipe, rather than semicolon by @KeithKelleher in #87
• Ramp3.0 newdb by @KeithKelleher in #88
• Ramp3.0 fix build errors by @andyptt21 in #90
• Ramp3.0 single name for ramp fast cata by @KeithKelleher in #92
• Add explicit parameters by @adtisch in #96
• Ramp3.0 kk fix by @KeithKelleher in #97
• Ramp3.0 plot updates by @mehtaky in #99
• fix filtering in chemicalClassEnrichment and chemicalClassSurvey by @KeithKelleher in #102
• Updated vignette link to newest one. by @Mathelab in #105
• Ramp3.0 replace mcall by @andyptt21 in #106
• merging in changes from ramp3.0 to my branch by @KeithKelleher in #107
• Ramp3.0 mysql refactor by @KeithKelleher in #109
• hand off sql formatting to the data access layer, instead of in rampFastCata by @KeithKelleher in #110
• analytes -> mets for Ontology functions by @adtisch in #112
• fix rampFastCata for older databases - before there was the common_name column by @KeithKelleher in #113
• changes to chemicalClassSurvery by @mehtaky in #114
• remove documentation pages for all non-exported functions by @KeithKelleher in #115
• fix broken link on readme by @KeithKelleher in #117
• fix getReactionClassesForAnalytes when multiRxnParticipantCount > 1, … by @KeithKelleher in #118
• Addition of runReactionClassTest & buildCataNetworkDatafarme by @mehtaky in #119
• fix getMetaFromOnto for inputs with special characters by @KeithKelleher in #120
• Ontology cleanup by @adtisch in #125
• Updates to Reaction Functions by @mehtaky in #123
• add two database queries to get the counts of chebi IDs and uniprot IDs by @KeithKelleher in #126
• Ramp3.0 pfocr by @KeithKelleher in #128
• Make all params cammelCase by @adtisch in #127
• Fixes for Enrichment Based Functions by @mehtaky in #130
• Small fixes: by @mehtaky in #131
• Ramp3.0 by @KeithKelleher in #135
• Update how similarity matrices are handled from the database by @KeithKelleher in #137
• Roxygen changes by @mehtaky in #138
• fix bug in getOntoFromMeta when using a list of names for the input by @KeithKelleher in #141
• Ontology Update AT Updated by @adtisch in #144
• development to support backwards compatability with user scripts. by @KeithKelleher in #145
• Ramp3.0 by @andyptt21 in #148
• Ramp3.0 fix compatability by @KeithKelleher in #149
• Made text size scale with longest pathway name in lollipop plot by @andyptt21 in #146
• Ramp3.0 fixes by @KeithKelleher in #152
• add new database with RefMet IDs by @KeithKelleher in #153
• Ramp3.0 - final updates by @Mathelab in #154
• Update README.md by @Mathelab in #155
• Update README.md by @Mathelab in #156

New Contributors

• @jorainer made their first contribution in #57
• @adtisch made their first contribution in #96

Full Changelog: v2.3.4...v3.0.2