- Update tests to latest testthat change.
- Added support for plots of similarities with
plot_data()andplot_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.
- Added alternative text to plots on vignettes.
- Reactivated again the comparison with GOSemSim
- Move to NEWS.md.
- Corrected "value of length: 2 type: logical".
- Avoid cropping the images.
- Updated documentation.
- Added a pkgdown website
- Exported inverseList function
- Improved spelling
- Corrected a bug related to logical coercion of length greater than 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
- 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
- Add methods for GeneSetCollections
- 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.
- Correct incorrect implementation of rcmax method
- Improving reciprocal method
- Increased testind of combineScores
- Adding combineScoresPar for high number of comparisons
- Improving the speed of mpathSim
- Removing the dependency of graph
- Add more test to increase coverage
- Document better the BiocViews.
- Accept named pathways in mpathSim
- Accept named genes in mgeneSim
- diceSim returns NA when not able to calculate similarities
- Increase test coverage
- 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)
- Add reciprocal method to combineScores
- Update documentation of combineScores
- Update documentation of combineScores
- Update documentation of combineScores
- Correct a test for clusterSim
- 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
- Update Vignette to just output html
- Submit the package to the Bioconductor project
- Add the Bioconductor webhook