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Version 0.2

WormBase 0.2.0 (2018-03-04)

  • Renamed package to wormbase from worminfo.
  • Simplified core functionality to simply pull genome annotations from the WormBase website into R.
  • Previous functionality querying the ENSEMBL, PANTHER, and EggNOG databases will be split out into organism-agnostic packages.
  • RNAi clone support is being migrated to the rnaiscreen package.

WormBase 0.2.1 (2018-04-18)

  • Renamed gene column to geneID where applicable.
  • Removed fs package dependency.
  • Added progress bars for functions that take a long time to load.

WormBase 0.2.2 (2018-04-23)

  • Broke out assertive imports into separate packages: assertive.properties, assertive.strings, assertive.types.
  • Removed todo comment in description.R file.

WormBase 0.2.3 (2018-07-21)

  • Fixed geneID() function to work with latest WormBase release that now returns an extra biotype column.
  • Removed internal parallel mclapply() calls in favor of pblapply() for better compatibility across platforms.

WormBase 0.2.4 (2018-11-21)

  • Maintenance release updating the package to require R 3.5.
  • Improved documentation for functions and rebuild pkgdown website.
  • Added progress = TRUE option for functions that can take a long time to parse data. Previously, this was always enabled but now can be disabled using this progress = FALSE. Note that invisible(capture.output(x)) also works to suppress progress bars.

WormBase 0.2.5 (2019-03-19)

  • Reworked progress bar handling via pbapply::pblapply. This is now disabled for all functions by default, but can be enabled with progress = TRUE. pbapply package is now declared in “Enhances:” rather than “Imports:”.
  • Switched all internal assert checks to goalie package from assertive.

WormBase 0.2.6 (2019-03-23)

WormBase 0.2.7 (2019-03-26)

  • Added support for WS269 release. Functions that parse files from the WormBase FTP server had to be modified to ensure only annotations matching N2 gene identifiers (e.g. WBGene) are returned.
  • Removed dir argument for all functions that parse files from WormBase FTP server. Files now always download to tempdir instead.
  • Improved internal tidyeval code where applicable, notably inside mutate calls using sym and := rlang functions.

WormBase 0.2.8 (2019-07-24)

  • Updated basejump dependency versions.

WormBase 0.2.9 (2019-08-29)

Major changes:

  • Functions now return DataFrame instead of tbl_df.
  • Updated R dependency to 3.6.
  • Reworked internal code to use base R / Bioconductor methods, instead of tidyverse / dplyr approach.

Minor changes:

  • Improved documentation and updated basejump dependency versions.

WormBase 0.2.10 (2020-01-03)

Minor changes:

  • Working example and unit test updates for description function, now that the corresponding file on the WormBase FTP server is no longer malformed. This has been fixed as of WS274.
  • Updated REST API queries to use “https://wormbase.org/rest”. Previously, this called “http://api.wormbase.org/rest”, which no longer works.

WormBase 0.2.11 (2020-01-26)

Major changes:

  • Renamed package from “wormbase” to “WormBase”.

Minor changes:

  • Updated basejump dependencies.
  • Now using cli package to display messages.

WormBase 0.2.12 (2020-07-23)

Minor changes:

  • Maintenance release, updating R dependency to 4.0.