bioverbs 0.2.0 (2019-07-23)

Bumped version to v0.2 release series to match update conventions defined in other basejump packages, in preparation of a new release candidate that may be suitable for Bioconductor submission.

New functions

  • plotCountsCorrelation and plotCountsCorrelationHeatmap: New utility generics for comparing count correlation across multiple datasets.

Major changes

  • Renamed syntactic name functions, including "*Case" where appropriate. camel to camelCase; kebab to kebabCase; snake to snakeCase; upperCamel to upperCamelCase. The shorthand variants will remain exported in the syntactic package.

bioverbs 0.2.1 (2019-08-05)

New functions

  • Added plotCells generic.
  • Added cpm and tpm generics, which are defined in SingleCellExperiment.

Major changes

  • Deprecated clusterID generic in favor of clusters.

bioverbs 0.2.2 (2019-08-07)

Minor changes

  • plotCellTypesPerCluster: Added markers to signature.

bioverbs 0.2.3 (2019-08-08)

New functions

  • Added calculateMetrics generic, which was previously defined as a standard function in bcbioSingleCell package. This verb is also applicable to the Chromium package, so we have migrated it here.

bioverbs 0.2.4 (2019-08-08)

Reworked some verbs to support changes in acidplots and pending bcbioSingleCell update.

New functions

  • plotCountsPerCell.
  • plotCountsVsFeatures.
  • plotFeaturesPerCell.

Deprecated functions

  • plotGenesPerCell to plotFeaturesPerCell.
  • plotGenesDetected to plotFeaturesDetected.
  • plotUMIsPerCell to plotCountsPerCell.
  • plotUMIsVsGenes to plotCountsVsFeatures.

bioverbs 0.2.5 (2019-08-12)

New functions

  • plotSums: Utility generic for plotting row and column sums of a matrix.

bioverbs 0.2.6 (2019-08-23)

New functions

  • nonzeroRowsAndCols: Generic that allows for easy subsetting of non-zero rows and columns from an object.

bioverbs 0.2.7 (2019-08-27)

Major changes

  • Updated R dependency to 3.6.

New functions

  • Deprecated meltCounts in favor of simply using melt. Note that reshape2::melt is deprecated in favor of tidyr::gather, so we’re not conflicting with any activate tidyverse verbs here.
  • Migrated join, mutate, and select generics defined in transformer. Tightened up the required signature arguments here.

bioverbs 0.2.8 (2019-09-03)

Minor changes

  • Improve DataFrame return consistency in documentation.

bioverbs 0.2.9 (2019-09-09)

Major changes

  • Migrated syntactic generics to the syntactic package. This includes: camelCase, capitalize, dottedCase, kebabCase, snakeCase, upperCamelCase.
  • Made flatFiles defunct in favor of coerceS4ToList usage.

bioverbs 0.2.10 (2019-09-10)

New functions

  • Added contrastName<- assignment method generic.
  • Added resultsNames<- assignment method generic.