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Version 0.5

basejump 0.5.0 (2018-04-13)

New functions:

  • emptyRanges enables easy creation of placeholder ranges for GRanges objects, where transgene and FASTA spike-ins are needed.
  • hgnc2gene enables easy mapping of HGNC to Ensembl gene identifiers.
  • mgi2gene enables easy mapping of MGI to Ensembl gene identifiers.
  • panther function enables easy querying of the PANTHER website. Human, mouse, nematode worm, and fruit fly are currently supported. The specific PANTHER release (e.g. 13) can be declared using the release argument. Otherwise, the function will return the most recent annotations from the PANTHER website.
  • Added isURL check function.
  • readJSON adds support for JSON files. Like the other read functions, it supports both local files and remote URLs.

ggplot2 themes:

  • theme_midnight and theme_paperwhite provide minimal, high contrast ggplot2 themes with bold sans serif labels.

Major changes:

  • loadData now supports .rda, .rds, and .RData files. The function will error by design if multiple data extensions are detected inside the directory specified with the dir argument.

Minor changes:

  • Consolidated assert check function code.
  • Moved assertive imports to basejump-package.R file.
  • Consolidated globals inside package to globals.R file.
  • Removed internal .biocLite function. Now using requireNamespace instead, without attempting to install automatically.
  • Added internal support for safe loading RDS files.
  • Switched back to using message, warning, and stop instead of the rlang equivalents.
  • Improved internal method declaration using getMethod where applicable.
  • multiassignAsEnvir is now recommended in place of multiassignAsNewEnvir.
  • readFileByExtension will now attempt to use the rio package for file extensions that are not natively supported.
  • writeCounts now uses mapply internally.
  • Migrated assertFormalAnnotationCol to bcbioBase package.

basejump 0.5.1 (2018-04-16)

Minor changes:

  • emptyRanges: Now using match.arg internally to capture seqname argument.
  • Removed legacy .assignCamelArgs and .assignCamelFormals internal functions.
  • Improved internal handling of XLSX files in localOrRemoteFile.

basejump 0.5.2 (2018-04-26)

Minor changes:

  • Improved documentation for assert check functions.
  • Deprecated geomean in favor of geometricMean.
  • Simplified internal code for grepString.
  • Added message during hgnc2gene call.
  • Miscellaneous documentation fixes.
  • Moved internal constructors into the S4 method definitions, where applicable.
  • Simplified default parameter definition for panther(organism = "XXX").
  • Improved code coverage, using nocov where appropriate.

basejump 0.5.3 (2018-04-30)

Minor changes:

  • Improved internal S4 method code for fixNA and removeNA.
  • Tweaked gray accent colors in theme_midnight and theme_paperwhite. Now using British spelling internally for ggplot code.
  • Improved strip.background for theme_paperwhite, removing the black box around the labels when facet wrapping is enabled.

basejump 0.5.4 (2018-05-08)

basejump 0.5.5 (2018-05-15)

Major changes:

  • readGFF now uses rtracklayer::import internally to return GFF file as a GRanges object instead of a data.frame.

Minor changes:

  • assertIsGFF and parseGFFAttributes functions are now defunct.
  • Simplified internal GFF handling code for makeGRangesFromGFF, makeGene2symbolFromGFF, and makeTx2geneFromGFF.

basejump 0.5.6 (2018-05-19)

Minor changes:

  • Fixed NAMESPACE issue with GenomeInfoDb::seqnames.
  • Improved readGFF working example to reflect switch to GRanges return.
  • Added macOS bioc-release image to Travis CI build checks.

basejump 0.5.7 (2018-05-24)

Minor changes:

  • Tweaked gray color accents for theme_midnight and theme_paperwhite.

basejump 0.5.8 (2018-06-05)

Minor changes:

  • makeGRangesFromEnsembl now supports remapping of UCSC genome build to Ensembl. However, this isn’t recommended, and will warn the user.
  • convertUCSCBuildToEnsembl now returns NULL instead of erroring on genome build match failure.
  • stripTranscriptVersions now matches “.”, “-”, and “_” version delimiters.
  • Made unused dynamicPlotlist function defunct.
  • Consider deprecating assertIsCharacterOrNULL and assertIsDataFrameOrNULL in a future release.

Infrastructure changes:

  • Reenable Travis CI blocklist, excluding develop branch from checks.
  • Reorganized documentation of deprecated and defunct functions.

basejump 0.5.9 (2018-06-12)

Minor changes:

  • Markdown function consistency improvements. Now all relevant Markdown functions use text as the primary argument, instead of object.

basejump 0.5.10 (2018-06-28)

Minor changes:

  • Removed makeNames argument from readFileByExtension function. Use the makeNames family of functions manually after data import instead. This helps avoid unwanted sanitization of data.
  • Simplified assert checks for internal load function.
  • Improved code coverage.
  • AppVeyor CI updates to work with Bioconductor 3.8 devel.

basejump 0.5.11 (2018-07-09)

Minor changes:

  • Now requiring ggplot2 v3.0 internally.
  • theme_midnight and theme_paperwhite now extend ggplot2::theme_linedraw, improving the consistency between these themes.
  • Example data is now consistenly formatted using snake case: rnaseq_counts and single_cell_counts, instead of the previous camel case conventions: rnaseqCounts, singleCellCounts.
  • Camel variants of the ggplot themes are now deprecated.
  • Updated internal gene synonyms data from NIH.