basejump 0.10.0 (2019-03-28)

Major changes

  • Split out Ensembl (AnnotationHub/ensembldb) annotation processing and GFF/GTF file loading utilites to new freerange package. All of these functions remain re-exported here in basejump. This includes: annotable, convertUCSCBuildToEnsembl, detectOrganism, emptyRanges, makeGRangesFromEnsDb, makeGRangesFromEnsembl, makeGRangesFromGFF, makeGRangesFromGTF.
  • Split out heatmap functions to firestarter package. This includes plotHeatmap, plotCorrelationHeatmap, and plotQuantileHeatmap.
  • Split out all ggplot2 functions to new minimalism package.

Minor changes

  • Offloaded removeNA and sanitizeNA code to brio package, so these functions can be imported in thew new freerange package.
  • Moved organism_mappings internal dataset to freerange package.

basejump 0.10.1 (2019-04-01)

New functions

  • rankedMatrix: New utility function for quickly performing ranked matrix calculations. Particularly useful for differential expression comparison across studies using log2 fold change or Wald test statistic.

Minor changes

  • Simplified reexport methods for functions that define S4 methods.

basejump 0.10.2 (2019-04-07)

Major changes

  • aggregateRows, aggregateCols, aggregateCellsToSamples: Improved internal code for SummarizedExperiment metadata handling. Applies primarily to colData and rowData juggling for these methods.
  • interestingGroups: Reworked to define method against Annotated class. SummarizedExperiment inherits from this class, supporting metadata.
  • mapCellsToSamples: Tightened up match assert checks.
  • mcolnames now uses S4 methods, primarily against Vector class.
  • organism: Reworked S4 methods. Added support for Annotated and DataTable classes from S4Vectors.

Minor changes

  • Added additional unit tests, to improve code coverage.
  • Now covering the aggregation functions in better detail, using a minimal SingleCellExperiment object that works with aggregateCols.
  • Consistently use “acid” prefix instead of “basejump” for global options.
  • Miscellaneous working example improvements.
  • detectLanes: Renamed primary argument from object to path. Improved pattern formal to evaluate lanePattern global.
  • For S4 generators, renamed test paramter from basejump.test to acid.test.
  • sampleData: Improved error message when sampleName factor column is missing.
  • zeroVsDepth now returns depth column as integer instead of numeric.

basejump 0.10.3 (2019-04-07)

Minor changes

  • Bug fix release for freerange update. emptyRanges format has been renamed from mcolsNames to mcolnames.

basejump 0.10.4 (2019-04-22)

Major changes

  • meltCounts: Switched from using nonzeroGenes formal approach to minCounts and minCountsMethod, which is more flexible.

Minor changes

  • Consolidated minimalism and firestarter code into acidplots package.
  • Improve global options defined in formalsList.
  • Added back basejump vignette.

basejump 0.10.5 (2019-04-25)

Minor changes

  • Reworked S4 generic reexport method, in an attempt to get pkgdown to build vignette correctly. Otherwise, sampleData is erroring.

basejump 0.10.6 (2019-04-29)

New functions

  • showHeader: Utility function for show methods defined in other packages.

Minor changes

  • Updated basejump dependencies (see DESCRIPTION for details).

basejump 0.10.7 (2019-04-30)

New functions

  • Added method support for alphaThreshold and lfcThreshold against Annotated class. These values get stored in the metadata slot of the object.

basejump 0.10.8 (2019-05-05)

Major changes

  • Now pinned to R >= 3.5.

basejump 0.10.9 (2019-05-29)

Minor changes

  • Relaxed the deprecations on some functions to provide backward compatibility support for bcbioBase and bcbioRNASeq packages: readFileByExtension, readYAML, fixNA.
  • Now ensuring theme_midnight and theme_paperwhite are deprecated but exported with support, by suggesting acidplots package.
  • Added back defunct function warnings: assertHasRownames, tx2geneFromGFF.