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.