PEIMAN2 v1.1.0

PEIMAN2 1.1.0

This release adds support for external PEIMAN2 database updates while keeping the bundled database as the default. Users can now download and cache updated PEIMAN database files and UniProt PTM lists using update_peiman_database().

Analysis functions can use the bundled database, the latest cached database, or a specific dated database version for reproducible analyses. The mass spectrometry translation functions now also support selecting a cached UniProt PTM list version.

The default behavior remains CRAN-safe: package loading, examples, and standard checks continue to use the bundled internal data and do not require internet access.

Main changes

• Added update_peiman_database() for downloading and caching external data files.
• Added support for database_version in enrichment workflows.
• Added support for ptmlist_version in sea2mass() and psea2mass().
• Added loaders for cached PEIMAN database and UniProt PTM list versions.
• Updated README documentation with examples for using bundled, latest, and specific database versions.
• Added GitHub Actions workflow for R CMD check.

PEIMAN2 v1.0.1

Fixed the documentation for example dataset 2

PEIMAN2 v1.0.0

Updated DB to March 2025 version
Fixed some typos
Improved code quality

PEIMAN2 v0.1.1

Add proteins without any PTM to database
Add background list feature to SEA and PSEA
Remove dependency on tidyverse package and only include the required functions from dplyr etc
Some minor updates

PEIMAN2 v0.1.0

Update database - November version