Changes in version 1.1.3 (2022-06-26)
=====================================

* Added helper for plotting observed versus expected read counts (`getExpected()`)
* Added helper for plotting Bayes factors (`getBF()`)

Changes in version 1.1.2 (2022-06-06)
=====================================

* Added `codetools` to `Suggests` for `BiocParallel` dependency.

Changes in version 1.1.1 (2022-06-06)
=====================================

* Added support for running `edgeR` with `glmQLFTest` instead of `exactTest`.

Changes in version 0.99.8 (2022-02-14)
=====================================

* Fixed minor bugs with outdated arguments in the vignette.

Changes in version 0.99.7 (2022-02-14)
=====================================

* Changed `bp.param` argument to be called `BPPARAM` to be consistent with BiocParallel arguments.

Changes in version 0.99.6 (2022-02-09)
=====================================

* Corrected `future` reference in `README` to `BiocParallel`
* Changed ordering of arguments to put those without defaults first.

Changes in version 0.99.3 (2022-01-31)
=====================================

+ Documentation

  * Corrected typos, formatting errors, and missing links.
  * Modified `DESCRIPTION` to include `URL` and remove `Collates`
  * Removed directions for installing `PhIPData` in the `README` and Vignette.
  * Added package citations for `edgeR`.
  * Added package man page.
  * Additional details have been added to the documentation for `phipseq_model.bugs`.
  * Added citation.

+ Code

  * Standardized function names to use `camelCase`.
  * Standardized function arguments to use `dot.case`.
  * Though `edgeROne()` and `brewOne()` are not meant to be directly interfaced by the user, the two function names have been changed to reflect that they are still exported.
  * Renamed `edgeR()` to `runEdgeR()` to be more descriptive.
  * Corrected `paste0()` that should have been `file.path()`.
  * Converted to `BiocParallel` from `future` for parallelization support.

Changes in version 0.99.0 (2022-01-13)
=====================================

* Submitted to Bioconductor