basejump 0.1.2

  • Added bcbio plotQC() generic.
  • Added back toStringUnique() code, which is still in use in the worminfo package.
  • Added deprecations for summarizeRows() (now collapseToString()) and wash() functions.
  • Updated installation method to include manual installation of ensembldb. Otherwise, basejump installation fails due to GenomeInfoDb and GenomeInfoDbData not getting installed completely.
  • Now suggesting that the user installs suggested packages in the README.
  • Updated PANTHER annotation scripts.

basejump 0.1.1

  • Added overwrite support for saveData(). Now will skip on existing files when overwrite = FALSE.
  • Bug fix for readDataVersions(), which shouldn’t have the column types defined, using col_types = "ccT".
  • Improved key value pair method for loadDataAsName(). Now rather than using a named character vector for the mappings argument, the user can simply pass the key value pairs in as dots. For example, newName1 = "oldName1", newName2 = "oldName2". The legacy mappings method will still work, as long as the dots argument is a length of 1.
  • Ensembl release version now defaults to NULL instead of current for annotable(), gene2symbol(), symbol2gene() and tx2gene() functions.
  • Allow rowData to be left unset in prepareSummarizedExperiment(). This is useful for setting up objects that don’t contain gene annotations.
  • Removed sample selection by pattern matching (pattern, patternCol arguments) in readSampleMetadata(). This feature wasn’t fully baked and doesn’t offer enough functionality to the user.

basejump 0.1.0

  • Bump version to match bcbioRNASeq package.
  • Improved unit testing coverage of prepareSummarizedExperiment().
  • Added quiet mode support to functions that output messages, where applicable.
  • Moved roxygen function imports to each file from basejump-package.R file.
  • Deprecated sampleDirs() generic.
  • Improved organism detection in detectOrganism() and added support for chicken genome.
  • Clarified warning messages in prepareSummarizedExperiment() to make sample loading with loadRNASeq() and loadSingleCell() in the bcbio packages less confusing.
  • Improved NULL returns in readDataVersions, readLogFile(), and readProgramVersions() utility functions.
  • Fixed export of *GTF() alias functions to simply wrap the *GFF() functions with S4 methods support.
  • Improved lane split technical replicate handling in readSampleMetadataFile().
  • Improved camel() syntax for both lax and strict modes. Added upperCamel() function.
  • Switched str_() to base grep() and gsub() in internal functions.

basejump 0.0.25

  • 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.

basejump 0.0.24

basejump 0.0.23

basejump 0.0.22

  • 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 0.0.21

  • 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 .
  • 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 0.0.20

  • 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 0.0.19

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

basejump 0.0.18

basejump 0.0.17

basejump 0.0.16

  • 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 0.0.15

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

basejump 0.0.14

  • dplyr 0.7 NAMESPACE fixes and function tweaks.

basejump 0.0.13

  • setMethod on tidyverse NAMESPACE collisons (dplyr, tidyr) using `signature(“data.frame”).

basejump 0.0.12

  • Updated exports based on worminfo package.

basejump 0.0.11

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

basejump 0.0.10

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

basejump 0.0.9

  • Added snake_case function variants.

basejump 0.0.8

basejump 0.0.7

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

basejump 0.0.6

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

basejump 0.0.5

  • Consolidated functions in the documentation.

basejump 0.0.4

  • Improved documentation.

basejump 0.0.3

  • Removed dependencies and transfer functions to bcbioRNASeq.

basejump 0.0.2

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

basejump 0.0.1

  • Initial draft release.