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Changelog

Source: NEWS.md

Version 3.4.0

2024 Update

  • ProtWeaver and ProtWeb updated to EvoWeaver and EvoWeb (respectively)
  • Added some notes on correct package versions for use in this tutorial

Version 3.3.0

General Notes

  • First update after Bioconductor conference
  • Removes some material specific to conference workshop
  • Updates some graphics
  • Adds detailed description of runtime consideration

Version 3.2.0

General Notes

  • Changes example on Loading Genome Data to use a gene rather than random bases
  • Updates images for consistency
  • Minor edits to formatting

Version 3.1.0

General Notes

  • Adds information on using DECIPHER’s database API for working with big biological data
  • Switches to using base R plots for the phylogenetics section
  • Removes ape dependency

Version 3.0.0

General Notes

  • Version bump; code, writing, examples are presentation-ready aside from possible minor edits
  • All download buttons now working
  • Images all working
  • Minor formatting fixes

Version 2.2.0

General Notes

  • Download links fixed
  • IdTaxa training set now has a download link
  • Images added to each page

Version 2.1.0

General Notes

  • EvoWeaver analysis now uses the correct dataset
  • Conclusions page updated
  • IdTaxa training set fixed
  • Download links moved to be on each page

Future Work

  • Some download links still missing
  • Conclusions need more detail
  • Images missing

Version 2.0.0

General Notes

  • All examples except EvoWeaver analysis use the same dataset
  • IdTaxa now uses the correct training set

Future Work

  • EvoWeaver example will be updated
  • Conclusions section will be updated with actual takeaways
  • Writeup within each section will be changed to reflect new examples
  • Images will be added

Version 1.1.0

General Notes

  • Minor updates to wording and formatting
  • Corrections to Gene Calling and Annotation page
  • Tutorial section on Alignment-Free Analysis removed (will be readded later once I figure out where to put it)

Version 1.0.0

General Notes

  • All tutorials are now complete with dataset and code!

Future Work

  • Datasets will be updated prior to conference for consistency
  • Language/explanations will be updated
  • May include a photo of downloading dataset for FindingCOGs page

Version 0.7.0

General Notes

  • Adds download button in Setup page for datafiles
  • Minor formatting fixes and adjustments
  • Examples with TreeLine now use the correct version

Version 0.6.0

General Notes

  • Updates GeneCallingAnnotation with rough draft of code
  • Adds some new datafiles for use in tutorials

Version 0.5.0

General Notes

  • Updates LoadingGenomeData with code
  • Updates ConstructingPhylogenies with code
  • Updates CoevolutionNetworks with code

Known Issues

  • Data used in code examples is neither consisent nor final
  • Several tutorials still missing code

Version 0.4.0

Bugfixes

  • Updated some text to support pkgdown automatic reference linking
  • Minor updates to README

Version 0.3.0

General Notes

  • Updated tutorials with topics that will be covered in final product

Version 0.2.0

Bugfixes

  • Changes to fix display of buttons and pagination

Version 0.1.0

General Notes

  • Initialization of package
  • Creation of several empty files to mockup final layout