Changes in version 1.4.0 (2015-11-23) o Updated maintainer address Changes in version 1.3.0 (2015-03-07) o Added citation file o Added SimSeq paper to sources of SimData function o Added gene annotations to KIRC dataset o Add in vector of DE genes to output of SimData function Changes in version 1.2.0 (2014-12-10) o Set default norm factors estimation to 0.75 quantile of all counts o Removed edgeR dependency o Added in full TCGA KIRC dataset version 1.5.0 o Added in switch to change factor levels (treatment groups) around in SimData function o Updated documentations files Changes in version 1.1.0 o Updated SimData function to return columns used in sampling algorithm Changes in version 1.0.0 (2014-02-18) o Initial CRAN release Changes in version 0.5.2 o Updated package namespace to export and import variables o Changed depends to imports for edgeR and fdrtool o Fixed treatment output in function SimData o Removed algorithm from documentation for function SimData o Removed samp.col from output for function SimData o Changed treatment from 0 and 1 to non-tumor and tumor in kidney dataset Changes in version 0.5.1 o fixed bug in samp.independent method in SimData function when samp.independent equal TRUE o updated documentation Changes in version 0.5.0 o changed name of "offset" input to "norm.factors" in all functions o removed symmetric swapping functionally. As such n1.diff, n1.genes, and genes1.select are removed from all functions o Updated Documentation o Moved packages 'edgeR' and 'fdrtool's back to Depends field o updated demo file Changes in version 0.4.0 o Changed version names of all files from 1.x.y to 0.x.y o removed pval.hist function o now calculates weights for sampling genes by local fdr through fdrtool function from CRAN package 'fdrtool' o changed name of EBP input in SimData function to weights o updated examples for SimData o updated documentation of functions o removed package 'edgeR' from Depends field in description file o added package 'edgeR' and 'fdrtool' to Suggests field in description file Changes in version 0.3.0 o Moved wilcox signed rank and rank sum test out of SimData function to its own function, CalcPvalWilcox o Changed default for offsets to calcNormFactors from package 'edgeR' using method "TMM" o Created dependency on package 'edgeR' o Changed independence swapping code (changed method for adjusting data by offsets, eliminated for-loops) o Set samp.independent default to FALSE o Minimal cleaning up of help/documentation files (still needs a bit of work) o Created CalcPvalWilcox .Rd file Changes in version 0.2.0 o Substantially cleaned up code for readability and maintainability o Added more detailed comments to code o Renamed data.sim and sortdata functions to SimData and SortData respectively o Added samp.genes functions o Fixed errors in offset under the independent method section Changes in version 0.1.0 o Added symmetric swap functionality to data.sim function o Added checks on initial parameters submitted to data.sim function o help files are no longer working Changes in version 0.0.0 o Created sortdata, samp.col, and data.sim functions o sortdata: sorts matrix of gene express. data given vector of replicates and treatment o samp.col: samples replicates by columns separately and independently o data.sim: Now has functionality to simulate under both standard and independent method for both paired and unpaired data