  CHANGES IN VERSION 1.26.7

* Some URLs are reformatted in the documentations and vignettes.
* Data is only loaded into the function environment with `data(..., envir = environment())`.
* Namespace imports are adjusted to fixed the function name conflict.

===============================

  CHANGES IN VERSION 1.19.1

* We comply with changes in upstream dependency: PMCMR is replaced by PMCMRplus 
    and consecutively the function posthoc.kruskal.nemenyi.test.default() is 
    replaced by kwAllPairsNemenyiTest(). Also, in the package description, the 
    syntax for authors and maintainers is adapted to current requirements of 
    BiocCheck.

================================

  CHANGES IN VERSION 1.17.2

* We provide a new function LCD_extractCohort_callPerPID() which also belongs to 
    the LCD family and which performs the detection of signatures at cohort-wide 
    level, but re-runs the actual computation of the exposures per-PID with only 
    the signatures identified in the cohort-wide calling. The ovall wrapper 
    function LCD_complex_cutoff_combined() now also calls the new function and 
    stores the result in the returned list with item name 
    extractCohort_callPerPID 

================================

  CHANGES IN VERSION 1.17.1

* Introduction of an input parameter minimumNumberOfAlterations for the 
    functions LCD_complex_cutoff_perPID(), LCD_complex_cutoff_consensus() and
    LCD_complex_cutoff_combined(). If a sample has less mutations than this 
    cutoff, a warning is issued. By default, this values is set to 25 and may 
    be a good choice for analysis of SNV mutational signatures. For analysis of 
    Indel mutational signatures, a better choice is 20.

================================

  CHANGES IN VERSION 1.13.3

This is a stable version after several important changes.

* 95% Confidence intervals for exposures to mutational signatures can be 
    computed
* Analysis of the PCAWG mutational signatures is supported, both for PCAWG 
    SNV and PCAWG Indel signatures

The vignettes have been substantially changed:

* new vignettes have been written for the new features confidence intervals 
    and Indel signatures
* new vignettes were added for features already present in the package before,
    especially the optimal signature-specific cutoffs
* the topic of stratifiec analyses of mutational signatures was taken out of 
    the main vignette and now is described in a vignette on its own.

================================

  CHANGES IN VERSION 0.99.0

+ first version to be submitted to Bioconductor
