NEWS.md

In llrs/BioCor: Functional similarities

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

llrs/BioCor documentation built on Dec. 26, 2024, 11:52 a.m.