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Version 0.10

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.

basejump 0.10.10 (2019-06-08)

New functions:

  • matchEnsemblReleaseToURL: Takes an Ensembl release version (e.g. 96) as input and returns the corresponding archive URL.
  • matchHumanOrthologs: Convenience function that wraps biomaRt package to map model system gene identifiers to HGNC IDs and symbols. This is particularly useful for running orthologus GSEA with our pfgsea package.

Major changes:

  • combine method for SummarizedExperiment now includes all matrices defined in assays slot. Also improved support for colData handling on subsets where NA values have been removed.

Minor changes:

  • Gene2Symbol: Modified format formal to use “unmodified” instead of “long”, which is more intuitive.
  • makeGene2Symbol: Added support for format argument, similar to Gene2Symbol generator function.

basejump 0.10.11 (2019-07-17)

Minor changes:

  • Made theme_midnight and theme_paperwhite defunct, in favor if variants in new acidplots package.
  • Decreased the number of functions reexported from goalie package.
  • Updated basejump dependency package versions.
  • Improved Travis CI Docker configuration.

basejump 0.10.12 (2019-07-18)

Minor changes:

  • Bug fix for combine method on SummarizedExperiment. Needed to ensure row names are assigned on rowData to provide backward compatibility for Bioc 3.7.
  • Improved unit test exceptions on Docker and AppVeyor.
  • Improved installation instructions.
  • mapGenesToRownames: Improved matching for SummarizedExperiment objects that don’t contain gene-to-symbol mappings defined in rowData.
  • meltCounts: Improved factor handling. Also added matrix method support. Added advanced option to disable minCounts filtering, by setting as NULL.

Deprecations:

  • Tightened up the list of deprecated functions.