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NEWS
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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.