basejump 0.8.0 (2018-11-11)

Major changes

This release is the beginning of an attempt to rework the basejump codebase a bit and make the package easier to unit test on Travis CI. bcbio R packages will be pinned to v0.7.2 during this development period.

Here we are working to split out the functionality of basejump into several, smaller sub-packages:

  • basejump.annotations
  • basejump.assertions
  • basejump.classes
  • basejump.coercion
  • basejump.developer
  • basejump.experiment
  • basejump.generics
  • basejump.globals
  • basejump.io
  • basejump.markdown
  • basejump.plots
  • basejump.sanitization

basejump 0.8.1 (2018-11-15)

Major changes

The split-out sub-package approach isn’t working quite right, so the code base has been consolidated back into a single basejump package. Development toward splitting the package will continue, but a conceptual re-imagining of how to organize the functions is needed.

basejump 0.8.2 (2018-11-19)

Major changes

Migrating some additional base code that can be dispatched on either SummarizedExperiment or SingleCellExperiment from the bcbio R packages. We’re going to split out some of the single-cell RNA-seq functionality into separate packages, since a lot of my work moving forward deals with the 10X Genomics Cell Ranger platform, rather than the bcbio-supported inDrops platform.

In particular:

  • barcodeRanksPerSample.
  • filterCells.
  • plotBarcodeRanks.
  • plotCellCounts.
  • plotGenesPerCell.
  • plotMitoRatio.
  • plotMitoVsCoding.
  • plotNovelty.
  • plotReadsPerCell.
  • plotUMIsPerCell.
  • plotUMIsVsGenes.

Minor changes

  • Migrated some plotHeatmap and plotPCA code from bcbio R packages.
  • Added new formalsList global variable, which stashes getOption defaults used in some functions, namely the save/load functions and some plotting functions.
  • Switched to using formalsList along with formals declaration internally to make the parameters more consistent across functions.
  • Miscellaneous fixes to working examples and documentation.
  • Split out sanitization functions into separate R files (e.g. removeNA).

basejump 0.8.3 (2018-11-25)

Minor changes

  • Improved usage of assertthat::validate_that in S4 class validity checks. Removed former approach using internal .valid function.
  • Temporarily soft deprecated some functions that will be formally deprecated in a future release. See deprecated.R file.
  • interestingGroups doesn’t attempt validity check using validObject by default, which can be enabled instead using check = TRUE.
  • sampleData: Tightened up internal assert checks.
  • PANTHER: Minor tweaks to internal variable names inside .splitTerms.
  • transmit: Improved messages. Temporarily disabled working example, since it consistently fails on Travis CI.

basejump 0.8.4 (2018-11-28)

New functions

  • autopadZeros. Useful for padding zeros inside of a character vector.
  • basenameSansExt. Quickly get the basename without the file extension for desired file path(s). Surprisingly, this isn’t defined in the tools package so I wrote my own.
  • cleanSystemLibrary. I ran into some shared library configuration issues on the Azure infrastructure, so this utility function is useful for checking wheter an R installation has a clean library.
  • plotGenderMarkers: Migrated the SummarizedExperiment method from bcbioRNASeq package.

Minor changes

  • Split out call functions defined in calls.R into separate R files. Refer to dots, for example.
  • Split out environment.R into separate R files. See detectHPC for example.
  • Miscellaneous documentation improvements.

basejump 0.8.5 (2018-11-29)

New functions

  • relevelRowRanges, relevelColData.

Deprecations

  • markdownPlotlist. Renamed to markdownPlots.

Minor changes

  • autopadZeros: Improved internal code to keep track of names for character method. Also added method support for SummarizedExperiment, which works on the column names (e.g. sample names) only by default.
  • Ensembl2Entrez: Simplify validity check to require integer in entrezID column. Also reworked and improved internal code that supports run-length encoding (Rle) using decode.
  • export: Improved documentation for name argument.
  • makeGRangesFromEnsembl: Improved messages to user.
  • plotCountsPerBiotype: Improved error messages for when the biotype isn’t defined.
  • plotPCA: Add support for unique sample detection with areSamplesUnique, similar to the approach used in the bcbioRNASeq quality control R Markdown.
  • sampleNames: Simplified sampleName extraction, using [[ internally.
  • Miscellaneous documentation fixes.
  • Updated unit test for sanitizeRowData.

basejump 0.8.6 (2018-11-30)

Minor changes

  • Now importing hasUniqueCols from goalie. Switched from previous approach using areSamplesUnique.
  • Documentation improvement for genomeBuild, used in makeGRanges functions.
  • Miscellaneous documentation improvements to pass build checks.

basejump 0.8.7 (2018-12-01)

New functions

  • humanize. New generic that enables easy conversion to human-friendly column and/or row names. Useful for CSV file export in particular.

Minor changes

  • export: Added humanize argument support.
  • Improved grep pattern matching inside makeNames functions (e.g. .sanitizeAcronyms).
  • sampleData: Improved blacklist pattern matching against Seurat objects for SingleCellExperiment method.

basejump 0.8.8 (2018-12-03)

New functions

  • deg: Utility function to quickly obtain differentially expressed gene (DEG) identifiers as a character vector.

Major changes

  • plotHeatmap: Now defining row scaling internally, rather than relying on the functionality defined in pheatmap.