Skip to contents

Changelog

Source: NEWS.md

plasmoRUtils 1.1.3

In the latest release (1.1.3), an initial static code audit of plasmoRUtils v1.1.2 was conducted with assistance from OpenAI’s ChatGPT (GPT-6, October 2026). The tool was used to examine the R source code, identify potential bugs and implementation oversights, and suggest corrective changes.

All AI-generated findings and proposed modifications were subject to review by the package maintainer, who remains responsible for the final implementation, validation, and maintenance of the software.

Changes in version 1.1.3

New

  • getTableVeupathdb() enables you to fetch multiple fields from VEuPathDB given a vector of mixed identifiers from different species.
  • toGeneid() now uses getTableVeupathdb() function to perform desired ID mappings. Unidirectional mapping has been replaced with bidrectional mappings. Organism name and database name is no longer required.

Major fixes

  • easyTPM lacked reordering of gene info data frame w.r.t count matrix. This would lead to incorrect TPM normalization if user supplied gene lengths data frame without reordering rows w.r.t count matrix. This scenario is now handled.
  • easytopGO: The background geneset was being passed but was not used in enrichment analysis. This has been fixed now. A bug in the visualization function easyGOPlot was also fixed.

Documentation and vignette updates

  • Revised the tutorials against the version 1.1.3 function signatures, including explicit Fisher/KS input requirements, GO background, API-gated examples and non-ambiguous legacy/probe mappings.
  • Updated the README and vignette dependencies and corrected unsupported examples.

Minor fixes

  • easyGOPlot legend was being plotted incorrectly for some borderline cases. This has now been fixed.
  • Improved easymakeOrgdb function. Negative (NOT) GO annotations, invalid/unknown GO identifiers, and associations whose gene IDs do not match the GFF are excluded. API access is implemented.
  • API access also implemented in easyTxDbmaker.
  • Fixed temporary file creation and deletion in easyMCA.

Changes in version 1.1.2

  • VEuPathDB databases related functions were rewritten to enable usage of API keys for access. These include getPreconfiguredTable, getTable, getpairedOrthologs, listOrthomcl and listVeupathdb.
  • Added new function getTableAttributes to list attributes for customFields argument in getTable function.
  • Added caching capability in getPreconfiguredTableOrthomcl to reduce time for massive query and subsetting.
  • Fixed linking functions across documented help pages.

Changes in version 1.1.1

  • Improved error handling in searchTedConsensus function for marginal cases where uniprot IDs throws 404 error.
  • Error handling improved in easyAF2Signal for marginal cases like A0A140KXW6.
  • Deprecation of searchGSC due to compliance issues. This function has now been replaced with searchRS to query Research Square programmatically using its API.
  • Removed ggpubr, ggsci and glue to slim down package.
  • New function: getPreconfiguredTableOrthomcl() is a new function to fetch preconfigured tables from OrthoMCL. It can be used to map old OG IDs to new OG IDs, retrive tables of PFam Architecture of Each Protein, Summary of Pfam domains, Summary of EC Numbers etc.
  • Fixed latency in searchHP by using httr2.
  • Revised searchPM function by replacing depreciated functions with new functions.
  • Revised searchPhPl to handle borderline cases.

Changes in version 1.1.0

  • searchGSC function can now fetch articles for custom years of interest. Title translation to desired language provided. Users can choose how many pages to parse to match number of articles returned upon manual query in Google scholar.
  • searchHP : Taxon id is not mandatory but desired to avoid fetching interactions from other organisms having same gene name.
  • Help sections of functions improved.
  • New functions: getpairedOrthologs , listOrthomcl, listipdb to get paired orthologs from OrthoMCL 7 and InParanoiDB.
  • Functions removed: searchMT and easyPie were removed due to repeated failure given the database latency.
  • searchApicoTFdb now fetches more specialised tables from the database. searchIpDb is not Plasmodium specific and can accept uniprot IDs of other organisms provided by InParanoiDB.
  • searchPhPl was unable to fetch phenotypes for some genes. This has been fixed.

Changes in version 1.0.0

  • First stable release.

Changes in version 0.99.1

  • Vignettes created.

Changes in version 0.99.0

  • First version created.