Changes in version 1.0.2                        

Fixed error in tests

                        Changes in version 1.0.1                        

Updated allele names in the vignette after data package "scaeData" was
updated

                       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.