\name{NEWS}
\title{NEWS file for the \pkg{Uniquorn} bioconductor package }
\section{Changes in version 1.0.8 [2016-06-17]}{
    \subsection{Optimization confidence score}{
        \itemize{
            \item Fixed the installation of the package
        }
    }
}
\section{Changes in version 1.0.7 [2016-06-13]}{
    \subsection{Optimization confidence score}{
        \itemize{
            \item Optimized the way confidence scores are calculated to increase the sensitivity and specificity of the method 
        }
    }
}
\section{Changes in version 1.0.6 [2016-06-05]}{
    \subsection{Optimization of default confidence score}{
        \itemize{
            \item Adjusted default confidence score to optimal threshold 
        }
    }
}
\section{Changes in version 1.0.5 [2016-05-30]}{
    \subsection{Minor Bugfixes}{
        \itemize{
            \item Fixed errors connected to adding CLs
        }
    }
}
\section{Changes in version 1.0.4 [2016-05-27]}{
    \subsection{Introduction of confidence score}{
        \itemize{
            \item Confidence score is the central threshold now
            \item Default is 3.0
            \item The score is the negative log e of the q-value
        }
    }
}
\section{Changes in version 1.0.3 [2016-05-18]}{
    \subsection{Changes to treshold calculation}{
        \itemize{
            \item Fixed error in threshold calculation
        }
    }
}
\section{Changes in version 1.0.1 [2016-05-09]}{
    \subsection{Minor update of BED files}{
        \itemize{
            \item Extended length of BED file mutations shown in the IGV
        }
    }
}
\section{Changes in version 0.99.16 [2016-05-04]}{
    \subsection{Further minor update of statistics module}{
        \itemize{
            \item Further minor fixes to statistics
        }
    }
}
\section{Changes in version 0.99.15 [2016-05-03]}{
    \subsection{Minor Update of statistics}{
        \itemize{
            \item Minor fixes to statistics
        }
    }
}
\section{Changes in version 0.99.14 [2016-05-03]}{
    \subsection{Major Update of statistics}{
        \itemize{
            \item Replaced the absolute and relative cutoff with a p an q-value based on a binomial distribution
        }
    }
}
\section{Changes in version 0.99.13 [2016-04-08]}{
    \subsection{Fixed unit tests}{
        \itemize{
            \item Further update test suite
        }
    }
}
\section{Changes in version 0.99.12 [2016-04-08]}{
    \subsection{Fixed unit tests}{
        \itemize{
            \item Update testing suite
        }
    }
}
\section{Changes in version 0.99.11 [2016-04-01]}{
    \subsection{Fixed unit tests}{
        \itemize{
            \item Fixed error in unit tests
        }
    }
}
\section{Changes in version 0.99.10 [2016-03-30]}{
    \subsection{Added Unit tests}{
        \itemize{
            \item Added Unit test feature
        }
    }
}
\section{Changes in version 0.99.9 [2016-03-29]}{
    \subsection{Improved documentation}{
        \itemize{
            \item Minor documentation bugfixes.
        }
    }
}
\section{Changes in version 0.99.8 [2016-03-25]}{
    \subsection{Fixed Bug}{
        \itemize{
            \item General bugfixing.
        }
    }
}
\section{Changes in version 0.99.7 [2016-03-24]}{
    \subsection{Fixed Bug}{
        \itemize{
            \item Minor bugfix concerning output of CL identifications.
        }
    }
}
\section{Changes in version 0.99.6 [2016-03-23]}{
    \subsection{Fixed Bug}{
        \itemize{
            \item Minor bugfix concerning data parsing of CellMiner data.
        }
    }
}
\section{Changes in version 0.99.5 [2016-03-22]}{
    \subsection{Fixed Bug}{
        \itemize{
            \item Fixed a bug that lead to incorrect calculation of CoSMIC CLP CL mutation weights.
        }
    }
}
\section{Changes in version 0.99.4 [2016-03-16]}{
    \subsection{Added features}{
        \itemize{
            \item 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'
        }
    }
}

\section{Changes in version 0.99.3 [2016-03-02]}{
    \subsection{Fixed bugs}{
        \itemize{
            \item Fixed vigniette
        }
    }
}

\section{Changes in version 0.99.2 [2016-03-02]}{
    \subsection{Fixed bugs}{
        \itemize{
            \item Moved NEWS.Rd from 'Uniquorn' to 'Uniquorn/inst'
        }
    }
}

\section{Changes in version 0.99.1 [2016-03-02]}{
    \subsection{Fixed bugs}{
        \itemize{
            \item Fixed NEWS section
            \item Fixed unit testing
            \item Fixed the Vignette: replaced the github-dependent installation with the biocLite installation
        }
    }
}

\section{Changes in version 0.99.0 [2015-01-27]}{
    \subsection{New features}{
        \itemize{
            \item Identify cancer cell lines
            \item Show which cancer cell line are contained
            \item Show which mutations are annotated for selected cancer cell lines
            \item Show which mutaitons are overall included
            \item Parse cancer cell line custom data -> add your own samples and identify these
        }
    }
}