Changes in version 1.3.0 (2018-07-26) + Submitted to Bioconductor Changes in version 1.3.1 (2018-08-15) + Updated DESCRIPTION file o replaced Author and Maintainer by Authors@R o added URL for BugReports + Changed from manual NAMESPACE and *Rd files to a creation by roxygen2 + Changed function names for reading data from "load..." to "read..." + Shortened the longest function names o getGenomesFromMutationFeatureData -> getGenomesFromMutFeatData o getSignatureListFromEstimatedParameters -> getSignaturesFromEstParam + Used robust sequence creation with seq, seq_len, seq_along instead of 1:N etc + Consistent use of native class checking such as is.numeric() + Implemented wrapper functions for external classes which do not provide the necessary accessor functions + Replaced instances of sapply() and unlist(lapply()) by vapply() + Updated vignette and made most code chunks runnable + Added greedy search option to plotExplainedVariance (significant speed-up) Changes in version 1.3.2 (2018-08-29) + Fixed a minor bug in mapSignatureSets() that occurred when the two signature sets had the same size. + Added functions to verify the format of signatures, genomes and exposures: o isAlexandrovSet(), isShiraishiSet(), isSignatureSet() o sameSignatureFormat() o isExposureSet() + Moved description of deprecated BiocInstaller in vignette to BiocManager. Changes in version 1.3.3 (2018-09-24) + Implemented own signature plotting to remove code dependency from pmsignature + Decoupled the following data conversions functions from pmsignature code: o getGenomesFromMutFeatData() o getSignaturesFromEstParam() + Moved some common code to a new internal function for ease of maintenance. + Fixed bugs: o Error when some sequence names where not found in the reference genome, e.g., due to different names of decoy sequences. o Minor problems with unlikely signatures composed of only the mutated base (no flanking bases) Changes in version 1.99.0 (2018-11-10) + When transcription direction is taken into account: exclude mutations in regions with overlapping genes of opposing transcription directions by default! Previous versions of decompTumor2Sig took the approach of pmsignature, using the transcription direction of the first gene encountered in the transcript database (which is rather arbitrary); excluding these mutations appears more appropriate. The old approach can still be used with an additional function parameter. + Removed pmsignature from the suggested packages (not allowed in Bioconductor) + Reduced the number of tumor genome examples in extdata for faster processing and smaller package size (six out of 21 tumors from PMID:22608084) Changes in version 1.99.1 (2019-04-07) + Changed the procedure which converts lists of individual mutations from MPF files into tumor mutation profiles to reduce the memory footprint and allow for larger sets of tumors to be read from file. + When genomes are read from files: remove genomes without SNVs (no mutation frequencies) + Recognize indels for which either the REF or ALT base is specified as "-" + Fix bugs: o Error when quadprog returned a mutation frequency of minimally larger than 1 (which is theoretically impossible but can probably happen due to the rounding of floating point numbers) Changes in version 2.1.0 (2019-08-18) + adapted readAlexandrovSignatures to read the file format used by the COSMIC mutational signatures version 3 (May 2019; Single Base Substitution/SBS signatures only) Changes in version 2.4.1 (2020-07-27) + Removed dependency of package CRAN vcfR (archived on 2020-07-05), using functions of Bioconductor package VariantAnnotation instead + Improved the mutation filtering so that multiallelic SNVs aren't excluded when loading tumor genomes from a VCF file + Updated citation and affiliation information + Added consistency check for reference genome and genome annotation + Improved error messages