\name{NEWS}
\title{News for Package \pkg{scDD}}

\section{Version 1.1.7, (2017-10-23)}{
  \itemize{
    \item{A parameter 'level' was added to the main 'scDD' function which allows
    the user to control the significance level used as the cutoff for 
    considering a gene to be differentially distributed. Previously it was fixed
    at 0.05 (now the default value).}
    \item{Two columns were added to the results object that contain (1) an 
    overall combined p-value (via Fisher's method) for nonzero and zero 
    differences, and (2) Benjamini-Hochberg adjusted version of (1).}
    \item{If `testZeroes` is FALSE, the columns with p-values for the test of
    differential dropout are no longer included. Previously they held NA values}
    \item{If `testZeroes` is TRUE, all zero test p-values are included in the 
    output. Previously, only the tests where the nonzero test was not 
    significant were reported.}
  }
}

\section{Version 1.1.5, (2017-09-27)}{
  \itemize{
    \item{The input and output object of the main scDD function has been
     changed from SummarizedExperiment to SingleCellExperiment to increase
     interoperability among other Bioconductor packages}
    \item{The simulateSet function now returns a SingleCellExperiment object 
     (previously it returned an object in list format)}
    \item{The preprocess function now takes as input a SingleCellExperiment
     object instead of a list of data frames}
  }
}

\section{Version 1.0.0, Bioconductor 3.5 Release (2017-04-23)}{
  \itemize{
    \item{scDD is a package for identifying differentially distributed genes in
    single-cell RNA-seq data. It is designed to detect differences in 
    expression that are more complex than a simple mean shift, including:}
    \item{traditional differential expression (DE)}
    \item{differential modality (DM)}
    \item{differential proportion of cells in each state (DP)}
    \item{both differential modality and differential proportion (DB)}
  }
}

\section{Version 0.99.0 (2016-12-07)}{
  \itemize{
    \item Package prepared for Bioconductor submission.
  }
}
