Version 0.0

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)

• setMethod for tidyverse NAMESPACE collisons (dplyr, tidyr) using signature("data.frame").

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)

• Added annotables common code from bcbio packages.
• Added automatic file reading using readr package.
• Combined write counts functions from bcbioRNASeq and bcbioSinglecell.
• Initial commit of assign_data for use in bcbioSingleCell sample loops.

basejump 0.0.18 (2017-07-24)

• Initial support for SummarizedExperiment creation with packageSE.

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)

• Upgraded annotable function to query Ensembl using the ensembldb package rather than annotables.

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.