basejump 0.0.1 (2017-03-17)

  • Initial draft release.

basejump 0.0.2 (2017-03-22)

  • Added bcbio data import functions.
  • Added ggplot2 wrapper functions for quality control.

basejump 0.0.3 (2017-03-22)

  • Removed dependencies and transfer functions to bcbioRNASeq.

basejump 0.0.4 (2017-04-07)

  • Improved documentation.

basejump 0.0.5 (2017-04-12)

  • Consolidated functions in the documentation.

basejump 0.0.6 (2017-04-14)

  • Dependency fix for successful compilation on the HMS RC Orchestra cluster.

basejump 0.0.7 (2017-0422)

  • Bug fixes for dplyr 0.6.0 update and improved kable handling.

basejump 0.0.8 (2017-05-13)

  • Added back saveData utility functions.

basejump 0.0.9 (2017-05-13)

  • Added snake case function variants.

basejump 0.0.10 (2017-05-14)

  • Added NAMESPACE utilities to deal with tidyverse generic verbs.
  • Switched package documentation method to use roxygen2 with pkgapi.

basejump 0.0.11 (2017-05-18)

  • Improved naming functions to dynamically handle character vectors and objects that support naming assignments.
  • Added removeNA utility function.

basejump 0.0.12 (2017-05-25)

  • Updated exports based on wormbase package.

basejump 0.0.13 (2017-06-12)

basejump 0.0.14 (2017-06-13)

  • dplyr 0.7 NAMESPACE fixes and function tweaks.

basejump 0.0.15 (2017-06-18)

  • Added testthat support for lintr checks.
  • Added S4 generic for as_tibble.

basejump 0.0.16 (2017-06-28)

  • Minor NAMESPACE updates while working on bcbio packages.
  • Tweaks for tidyverse S4 generic verbs. In particular, as_tibble now provides better consistency for rowname conversion.

basejump 0.0.17 (2017-07-11)

basejump 0.0.18 (2017-07-24)

basejump 0.0.19 (2017-07-24)

  • Improved documentation and consistency with bcbio packages.
  • Improved integration of gene annotation calls using annotables package.

basejump 0.0.20 (2017-08-16)

  • Offloaded devtools functions to personal package.
  • Upgraded all functions to S4 functions where possible.
  • Assign utilities were kept as S3 functions since S4 dispatch makes parent.frame assignment not work correctly.
  • Deprecated snake case and British spelling variants to reduce the number of exported functions.
  • Added more working examples.
  • Added unit testing for annotables functions.

basejump 0.0.21 (2017-09-01)

  • NAMESPACE improvements. Reduced the number of re-exported functions to simplify the package.
  • Improved code coverage and unit testing with additional testthat checks. Specifically, added unit testing for remote download functions and improved testing for GTF file utilities.
  • Code coverage now above 90%!
  • Renamed packageSE to prepareSE for better semantic meaning.
  • Made multiple generics more flexible by inclusion of passthrough ().
  • Reduced the number of deprecated functions.
  • Initial commit of internal localOrRemote utility function.
  • Initial commit of prepareTemplate function.
  • Added additional data-raw/ scripts.
  • Added onLoad.R script back to ensure proper attachment of annotables data package.
  • Removed tidyverse S4 method support.
  • Improved remote file handling for readFileByExtension, readGTF, and readYAML functions.

basejump 0.0.22 (2017-09-08)

  • Improved unit testing coverage.
  • Renamed prepareSE to prepareSummarizedExperiment. Improved row and column name handling in the function. It now outputs more helpful diagnostic messages on error.
  • Reworked and simplified detectHPC function to allow for unit testing.

basejump 0.0.23 (2017-09-14)

basejump 0.0.24 (2017-10-10)

  • Added additional package version requirements in DESCRIPTION file.
  • Implicit integers are allowed.
  • Using GitHub version of covr package for unit tests.
  • Renamed multiassignAsNewEnv to multiassignAsNewEnvir
  • Added *GFF function variants for gene2symbolFromGTF and tx2geneFromGTF.
  • Added shared bcbio generic functions: aggregateReplicates, bcbio, bcbio<-, interestingGroups, metrics, plotGene, sampleDirs, sampleMetadata, selectSamples. These functions are saved in bcbioGenerics.R file.
  • Incorporated bcbio utility functions shared across bcbioRNASeq and bcbioSingleCell: readDataVersions (deprecated .dataVersions), readLogFile (deprecated .logFile), readProgramVersions (deprecated .programs), sampleYAML (deprecated .sampleYAML), sampleYAMLMetadata (deprecated sampleYAMLMetadata), sampleYAMLMetrics (deprecated .sampleYAMLMetrics).
  • Deprecated metadataTable function.
  • Moved all roxygen2 documentation to methods-*.R files where applicable.
  • Now using assays in prepareSummarizedExperiment generic definition as primary object.
  • Improved assignAndSaveData to add silent return of file path.
  • Now consistently using clear function definitions in chain operations with magrittr pipe (%>%).
  • Added .prepareSampleMetadata utility function, for use with loading sample metadata from an external CSV, Excel, or YAML file.
  • Added loadData functionality back to the package.
  • Initial commit of loadDataAsName function.
  • Improved annotable function documentation and support for Ensembl release versions.
  • Improved sanitization rules for camel, dotted, and snake name functions. Added the strict argument to camel and dotted.
  • Improved the documentation for the makeNames functions, by splitting each into their own separate methods file.
  • Improved S4 method support for the logRatio functions.
  • Added integer support for geomean function. Also improved internal code of geomean based on Paul McMurdie’s Stack Overflow post. See function documentation for more information.
  • Added release support for tx2gene functions.
  • Reduced the number of reexported functions (for documentation) down to the magrittr pipe (%>%), Matrix, DataFrame, and tibble.
  • Added silent return of file path to saveData function.
  • Improved documentation for tibble coercion using as(object, "tibble")
  • Renamed collapse function to collapseToString, to avoid NAMESPACE collisions with tidyverse packages (dplyr, glue).

basejump 0.0.25 (2017-10-13)

  • Improved consistency of setMethod calls using signature.
  • Converted loadRemoteData to a standard function instead of using S4 dispatch, allowing the envir argument to be set properly.