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Changelog

Source: NEWS.md

BioCor 1.28

  • Update tests to latest testthat change.

BioCor 1.26

  • Added support for plots of similarities with plot_data() and plot_similarity().
  • Removed internal data accidentally exposed (It was only used for testing).
  • Fix problem with documenting the package via roxygen2.
  • Remove the \describe{} macro used in some pages.

Changes in version 1.19.1

  • Added alternative text to plots on vignettes.
  • Reactivated again the comparison with GOSemSim

Changes in version 1.12

  • Move to NEWS.md.
  • Corrected “value of length: 2 type: logical”.
  • Avoid cropping the images.
  • Updated documentation.

Changes in version 1.10.1

  • Added a pkgdown website

Changes in version 1.8.1

  • Exported inverseList function
  • Improved spelling
  • Corrected a bug related to logical coercion of length greater than 1.

Changes in version 1.6.1

  • Corrected an empty condition in mclusterGeneSim
  • Corrected a logical check in mclusterSim
  • Improved coherence in the output between lists and GeneSetCollections
  • Added links between vignettes

Changes in version 1.5.4

  • Improved spelling
  • Reduced the complexity fo combineScoresPar and combineScores.
  • Improve efficiency of code in vignettes.
  • Change the news section
  • Adding a section about GeneOverlap package.
  • Changed the License

Changes in version 1.3.3

  • Add methods for GeneSetCollections

Changes in version 1.1.12

  • Improve speed on geneSim and clusterSim
  • Add a vignette describing more uses of BioCor
  • Adding more tests
  • Calculating similarities correctly when non-existent genes are provided.

Changes in version 1.1.4

  • Correct incorrect implementation of rcmax method

Changes in version 1.1.3

  • Improving reciprocal method
  • Increased testind of combineScores

Changes in version 1.1.0

  • Adding combineScoresPar for high number of comparisons
  • Improving the speed of mpathSim
  • Removing the dependency of graph

Changes in version 0.99.33

  • Add more test to increase coverage
  • Document better the BiocViews.

Changes in version 0.99.32

  • Accept named pathways in mpathSim
  • Accept named genes in mgeneSim
  • diceSim returns NA when not able to calculate similarities
  • Increase test coverage

Changes in version 0.99.31

  • Refer to weighted.mean in weighted help page
  • Change the default behaviour of mpathSim: now methods is NULL
  • Correct the misleading use of geneSetsCollection.
  • Add test for when large number of pathways are needed (pathSims_matrix)

Changes in version 0.99.30

  • Add reciprocal method to combineScores

Changes in version 0.99.30

  • Update documentation of combineScores

Changes in version 0.99.29

  • Update documentation of combineScores

Changes in version 0.99.28

  • Update documentation of combineScores

Changes in version 0.99.27

  • Correct a test for clusterSim

Changes in version 0.99.26

  • Update the required R version from 3.3 to 3.4’s
  • Adding more tests to increase the coverage
  • Using mpathSim to calculate path similarities

Changes in version 0.99.25

  • Update Vignette to just output html

Changes in version 0.99.24

  • Submit the package to the Bioconductor project

Changes in version 0.99.23

  • Add the Bioconductor webhook