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 Changes in version 0.99.8 (2022-02-14) ===================================== * Fixed minor bugs with outdated arguments in the vignette.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