NEWS

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signeR 2.5.1

• Preserve dimnames from the given input matrices

signeR 2.3.3

• Minor documentation fixes

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

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

signeR 2.1.1

• Fixed doc issues
• Fixed cpp issues

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

signeR 1.19.1

• migrate to PMCMRplus package

signeR 1.13.1

• fix issue with pseudo-variants on vcf

signeR 1.11.1

• ignore mutations on edges of chromosomes

signeR 1.9.3

• fix parsing issue in genCountMatrixFromVcf for some vcfs

signeR 1.9.2

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

signeR 1.9.1

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

signeR 1.7.1

• optimization of genCountMatrixFromVcf function

signeR 1.5.2

• support for generating matrices with a DNAStringSet

signeR 1.5.1

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

signeR 1.1.7

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

signeR 1.1.2

• Pre-calculate plot data during object construction

signeR 1.0.0

• First Bioconductor release.

signeR 0.99.17

• Reduced memory usage.