Changes in version 0.99.5                        

Changes regarding the second round of comments during the Bioconductor
submission review:

  - Minor changes to SCAE-show method

  - Extended and moved installation-checks for packages used in optional
    functionalities to the SCAE-constructor

  - Extended checks for the rowData setter

  - Extended unit tests to increase coverage

                       Changes in version 0.99.4                        

Changes regarding the first round of comments during the Bioconductor
submission review:

Removed multiple dependencies, now listed as suggested

  - computation of the logcounts assay now optional

  - computation of a knee plot and according inflection/knee points now
    optional

  - computation of new gene-symbols now optional

  - minor changes in tests (needs to be extended to test for new
    optional code); also extension of the tests to check new code

  - major changes in package structure and organisation

  - reworked vignette to include optional features

                       Changes in version 0.99.3                        

  - retriggering bioc build during package submission.

                       Changes in version 0.99.2                        

  - minor changes in the vignette to reduce build-time. Content is the
    same.

                       Changes in version 0.99.1                        

  - minor changes made regarding the Bioconductor submission review of
    scaeData which also affected this package.

                       Changes in version 0.99.0                        

  - The package is defining a S4 class that is extending the
    SingleCellExperiment class. The multi-layer data structure
    integrates data for immune genes at allele and functional level.

  - Workflow: To be able to generate a SingleCellAlleleExperiment object
    the data has to be generated by the connected workflow single-cell
    ImmunoGenomic Diversity (scIGD) which performs allele typing and
    quantification of genes and typed alleles. Use the
    read_allele_counts() function to read in the data and generate an
    SCAE object. This function also offers parameters to perform
    filtering on the data, as well as visualize the filtering step in a
    so called knee plot.