Changes in version 2.11.2                        

    o   Move VariantAnnotation from Depends to Imports

                       Changes in version 2.11.1                        

    o   Remove survivalAnalysis dependency

    o   Fixes for some ggplot2 warnings

    o   Update C++ req to C++14

                        Changes in version 2.5.1                        

    o   Preserve dimnames from the given input matrices

                        Changes in version 2.3.3                        

    o   Minor documentation fixes

                        Changes in version 2.3.2                        

    o   New function: genCountMatrixFromMAF, to generate a count matrix from a MAF file

    o   support for reading MAF files on signeRFlow

    o   support for utilizing any BSgenome on signeRFlow

                        Changes in version 2.3.1                        

    o   Moved the source repository to TojalLab

    o   Fixed issue when running with fixed signatures matrix

    o   Reduced the maxeval time in rare cases when there is no convergence

                        Changes in version 2.1.1                        

    o   Fixed doc issues

    o   Fixed cpp issues

                        Changes in version 2.0.0                        

    o   interactive shiny interface: signeRFlow

    o   Option to work with previously defined signatures, just estimating exposures.

    o   Parallel processing,

    o   New method to find the number of signatures (or groups) present in data, based on statistical testes of BIC values,

    o   Tests of signature association with survival data or continuous variables,

    o   Exposure-based clustering methods

                       Changes in version 1.19.1                        

    o   migrate to PMCMRplus package

                       Changes in version 1.13.1                        

    o   fix issue with pseudo-variants on vcf

                       Changes in version 1.11.1                        

    o   ignore mutations on edges of chromosomes

                        Changes in version 1.9.3                        

    o   fix parsing issue in genCountMatrixFromVcf for some vcfs

                        Changes in version 1.9.2                        

    o   fix for genCountMatrixFromVcf fails with phased genotypes

    o   added one-vcf-per-sample example to vignette

                        Changes in version 1.9.1                        

    o   fix prototype mismatch issue

    o   fix plot error: non-finite ylim when pvalue=0

                        Changes in version 1.7.1                        

    o   optimization of genCountMatrixFromVcf function

                        Changes in version 1.5.2                        

    o   support for generating matrices with a DNAStringSet

                        Changes in version 1.5.1                        

    o   fix GRanges list usage

    o   fix conflicts of NMF:seed, by adding VariantAnnotation to Depends before NMF

                        Changes in version 1.1.7                        

    o   Reorder method was renamed to Reorder_signatures.

    o   New methods Reorder_samples and Reorder_mutations was added.

                        Changes in version 1.1.2                        

    o   Pre-calculate plot data during object construction

                        Changes in version 1.0.0                        

    o   First Bioconductor release.

                       Changes in version 0.99.17                       

    o   Reduced memory usage.