Changes in version 1.3.3                        

NEW FEATURE

  - plot_gene_express() now has option to add label points with
    parameter label_points.

                        Changes in version 1.3.2                        

NEW FEATURES

  - findMarkers_1vAll() now only returns standardized log fold-change
    values, which cuts default run time roughly in half. A new parameter
    raw_logFC has been added; when TRUE, it yields the old behavior of
    returning both versions of the log fold-change.
  - findMarkers_1vAll() can now be parallelized with near-linear speedup
    via a new BPPARAM parameter.

                        Changes in version 1.3.1                        

NEW FEATURES

  - get_mean_ratio() has a new BPPARAM parameter allowing
    parallelization. Run time without parallelization was also
    marginally improved.

                        Changes in version 1.1.5                        

BUG FIXES

Correct (est_prop/est_prop_test) data usage after changes in v1.1.4

                        Changes in version 1.1.4                        

BUG FIXES

Package BisqueRNA is no longer a suggested dependency (no longer
available on CRAN).

Vignette "Deconvolution Benchmark in Human DLPFC" now loads pre-computed
est_prop data instead of running Bisque deconvolution.

                        Changes in version 1.1.3                        

NEW FEATURES

  - plot_gene_express() now has the option to use "free_y" axis.

                        Changes in version 1.1.2                        

NEW FEATURES

  - plot_gene_express() now has the option to change plot_type to
    'violin' or 'boxplot'

                        Changes in version 1.1.1                        

BUG FIXES

  - get_mean_ratio() was initially coercing sparse matrices into in
    memory matrices. We resolved this by using
    MatrixGenerics::rowMeans() and MatrixGenerics::rowMedians(). This
    issue was reported by @cyntsc.

                       Changes in version 0.99.0                        

NEW FEATURES

  - Initial version of DeconvoBuddies that introduces the Mean Ratio
    method for identifying cluster marker genes as implemented in
    get_mean_ratio(). This method is described in more detail at
    https://doi.org/10.1101/2024.02.09.579665. This package also
    provides a wrapper to scran::findMarkers() for identifying marker
    genes expressed in one cluster compared to all remaining ones. See
    findMarkeres_1vAll() for more details. Additionally, DeconvoBuddies
    provides plotting functions for visualizing gene expression as
    violin plots across different clusters. These plots are much smaller
    in size compared to other ones you can make with
    scater::plotExpression(). See plot_gene_express(),
    plot_marker_express(), and related functions.