Changes in version 1.2.0                        

  - Add options to generate violin plots instead of boxplots

  - Add support for Jenks natural breaks and custom grouping to
    step7TopGenesSurvival

  - Add support for custom regions and MotifDb filtering options to
    step7LinkedDNAMethylationSitesMotifSearching

  - step7TopGenesUserPeakOverlap now accepts peak names, generates
    results for each individual peak rather than each peak file, and
    accepts multiple input objects or directories

  - External genomic region files can now be provided as a list of
    multiple files and/or directories containing them, not just a
    directory

  - In step7TopGenesSurvival, remove parentheses from the names of
    several output variables, which complicated their use in some
    situations, and remove underscores from the plot legend labels

  - Fix TENETSavedSizePlot bug that caused warnings and failure to
    respect an explicitly specified size

  - Fix TENETCacheAllData to fail if any dataset does not exist on the
    hub

  - Significant documentation improvements

  - Do not suggest installing the development version of Bioconductor to
    use the stable version of the package, since it is no longer
    necessary

  - Update installation instructions for Ubuntu 24.04 and add a missing
    required package

  - Add a dependency on ggplot2 4.0 because the example
    MultiAssayExperiment object now requires it

  - Add CITATION file

                        Changes in version 1.1.1                        

  - Merge survival bug fix from Bioconductor 3.21 release branch; see
    below

                        Changes in version 1.1.0                        

  - Release generated automatically by Bioconductor - no changes

                        Changes in version 1.0.1                        

  - Fix typo in survival calculation code which made the number of case
    samples with intermediate expression/methylation levels always 0

                        Changes in version 1.0.0                        

  - Initial Bioconductor release