Changes in version 1.99.3 (2018-01-03): Bioconductor compliance o Minor modifications to comply with Bioconductor regulations Changes in version 1.99.2 (2018-20-02): Added RNA-seq and panel-seq capability o Some more minor bugfixes Changes in version 1.99.1 (2018-12-02): Added RNA-seq and panel-seq capability o Minor bugfixes Changes in version 1.99.0 (2018-15-01): Added RNA-seq and panel-seq capability o Modified the package to work with large scale RNA-seq and small scale panel-seq data o Please note that this might break custom libraries. In case of questions please contact the author Changes in version 1.4.2 (2017-15-05): Added critical scripts o Added a script to parse vcf files in a non-parallelized fashion. Changes in version 1.4.1 (2017-12-05): Fixed yet another penalty function bug o Fixed critical bug which disabled identifying CCLs in single-thread mode. Changes in version 1.3.1 (2016-28-11): Fixed yet another penalty function bug o Fixed rather major bug that led to too high penalty scores. Changes in version 1.1.3 (2016-28-11): Fixed penalty function bug o Fixed minor bug that led to incorrect penalty score calculation. Changes in version 1.1.2 (2016-28-11): Change of penalty function o The function that measures random background-noise matches and calculates a threshold above the background strength has been updated to be more strict. Changes in version 1.1.1 (2016-10-18): Change of default inclusion threshold o the new default inclusion weight has been set to 0.5 to optimally fit the new probabilistic model of version 1.0.9. Changes in version 1.0.9 (2016-10-11): Re-engineering of probabilistic model o The likelihood to observe a mutation/ variant in a query that matches a reference CCL's variant has been changed. The likelihood was 1 / #all variants in library and is now set to # number of variants in reference CCL / #all variants in library Changes in version 1.0.8 (2016-06-17): Optimization confidence score o Fixed the installation of the package Changes in version 1.0.7 (2016-06-13): Optimization confidence score o Optimized the way confidence scores are calculated to increase the sensitivity and specificity of the method Changes in version 1.0.6 (2016-06-05): Optimization of default confidence score o Adjusted default confidence score to optimal threshold Changes in version 1.0.5 (2016-05-30): Minor Bugfixes o Fixed errors connected to adding CLs Changes in version 1.0.4 (2016-05-27): Introduction of confidence score o Confidence score is the central threshold now o Default is 3.0 o The score is the negative log e of the q-value Changes in version 1.0.3 (2016-05-18): Changes to treshold calculation o Fixed error in threshold calculation Changes in version 1.0.1 (2016-05-09): Minor update of BED files o Extended length of BED file mutations shown in the IGV Changes in version 0.99.16 (2016-05-04): Further minor update of statistics module o Further minor fixes to statistics Changes in version 0.99.15 (2016-05-03): Minor Update of statistics o Minor fixes to statistics Changes in version 0.99.14 (2016-05-03): Major Update of statistics o Replaced the absolute and relative cutoff with a p an q-value based on a binomial distribution Changes in version 0.99.13 (2016-04-08): Fixed unit tests o Further update test suite Changes in version 0.99.12 (2016-04-08): Fixed unit tests o Update testing suite Changes in version 0.99.11 (2016-04-01): Fixed unit tests o Fixed error in unit tests Changes in version 0.99.10 (2016-03-30): Added Unit tests o Added Unit test feature Changes in version 0.99.9 (2016-03-29): Improved documentation o Minor documentation bugfixes. Changes in version 0.99.8 (2016-03-25): Fixed Bug o General bugfixing. Changes in version 0.99.7 (2016-03-24): Fixed Bug o Minor bugfix concerning output of CL identifications. Changes in version 0.99.6 (2016-03-23): Fixed Bug o Minor bugfix concerning data parsing of CellMiner data. Changes in version 0.99.5 (2016-03-22): Fixed Bug o Fixed a bug that lead to incorrect calculation of CoSMIC CLP CL mutation weights. Changes in version 0.99.4 (2016-03-16): Added features o Minimum amount of matching mutations required for a positive prediction between query and training sample can now be manually adjusted in the 'identify_vcf_file' function using the parameter 'miminum_matching_mutations' Changes in version 0.99.3 (2016-03-02): Fixed bugs o Fixed vigniette Changes in version 0.99.2 (2016-03-02): Fixed bugs o Moved NEWS.Rd from 'Uniquorn' to 'Uniquorn/inst' Changes in version 0.99.1 (2016-03-02): Fixed bugs o Fixed NEWS section o Fixed unit testing o Fixed the Vignette: replaced the github-dependent installation with the biocLite installation Changes in version 0.99.0 (2015-01-27): New features o Identify cancer cell lines o Show which cancer cell line are contained o Show which mutations are annotated for selected cancer cell lines o Show which mutaitons are overall included o Parse cancer cell line custom data -> add your own samples and identify these