
Changes in signeR 2.11.2:

   * Move VariantAnnotation from Depends to Imports

Changes in signeR 2.11.1:

   * Remove survivalAnalysis dependency
   * Fixes for some ggplot2 warnings
   * Update C++ req to C++14

Changes in signeR 2.5.1:

    * Preserve dimnames from the given input matrices

Changes in signeR 2.3.3:

    * Minor documentation fixes

Changes in signeR 2.3.2:

    * New function: genCountMatrixFromMAF, to generate a count matrix from a MAF file
    * support for reading MAF files on signeRFlow
    * support for utilizing any BSgenome on signeRFlow

Changes in signeR 2.3.1:

    * Moved the source repository to TojalLab
    * Fixed issue when running with fixed signatures matrix
    * Reduced the maxeval time in rare cases when there is no convergence

Changes in signeR 2.1.1:

    * Fixed doc issues
    * Fixed cpp issues

Changes in signeR 2.0.0:

    * interactive shiny interface: signeRFlow
    * Option to work with previously defined signatures, just estimating exposures.
    * Parallel processing,
    * New method to find the number of signatures (or groups) present in data, based on statistical testes of BIC values,
    * Tests of signature association with survival data or continuous variables,
    * Exposure-based clustering methods

Changes in signeR 1.19.1:

    * migrate to PMCMRplus package

Changes in signeR 1.13.1:

    * fix issue with pseudo-variants on vcf

Changes in signeR 1.11.1:

    * ignore mutations on edges of chromosomes

Changes in signeR 1.9.3:

    * fix parsing issue in genCountMatrixFromVcf for some vcfs

Changes in signeR 1.9.2:

    * fix for genCountMatrixFromVcf fails with phased genotypes
    * added one-vcf-per-sample example to vignette

Changes in signeR 1.9.1:

    * fix prototype mismatch issue
    * fix plot error: non-finite ylim when pvalue=0

Changes in signeR 1.7.1:

    * optimization of genCountMatrixFromVcf function

Changes in signeR 1.5.2:

    * support for generating matrices with a DNAStringSet

Changes in signeR 1.5.1:

    * fix GRanges list usage
    * fix conflicts of NMF:seed, by adding VariantAnnotation to Depends before NMF

Changes in signeR 1.1.7:

    * Reorder method was renamed to Reorder_signatures.
    * New methods Reorder_samples and Reorder_mutations was added.

Changes in signeR 1.1.2:

    * Pre-calculate plot data during object construction

Changes in signeR 1.0.0:

    * First Bioconductor release.

Changes in signeR 0.99.17:

    * Reduced memory usage.
