CHANGES IN VERSION 1.11.2 ------------------------- o Added correct CITATION CHANGES IN VERSION 1.11.1 ------------------------- o Maintainer E-mail adress updated CHANGES IN VERSION 1.3.1 ------------------------- FEATURES o `summary()` output more concise o `getEnrichment()` takes `F` for specifying a desired foreground component for standardization of the enrichment o `iterations` argument allows running multiple fits with different starting values o T Filter threshold can now be specified with `minP` argument for less stringent filtering o Added a normR overview scheme to the vignette o Qvalue computation improvement by specifying range for prop. of H_0 BUGFIXES o Fixed the erroneous tiling of supplied GR objects in char,char,GRanges o `diffR()` is more robust by doing a label-switched fit also CHANGES IN VERSION 1.0.0 ------------------------- o Initial Bioconductor 3.3 Release CHANGES IN VERSION 0.99.7 ------------------------- BUGFIXES o Binning "genome" now reports correct genomic coordinates enrichR,character,character,data.frame-method diffR,character,character,data.frame-method regimeR,character,character,data.frame-method o Correcting counting on supplied ranges object with a warning displayed if they are not equally sized o getEnrichment() allows for adjusting the foreground now o T Filter threshold is now controlled with the minP argument in main methods CHANGES IN VERSION 0.99.6 ------------------------- FEATURES o summary() for NormRFit instances shows now percentage of bins at each significance level o getEnrichment() takes argument for computing a non-standardized enrichment PERFORMANCE o SIMD optimization for OpenMP >= ver4 CHANGES IN VERSION 0.99.5 ------------------------- FEATURES o summary() for NormRFit instances of types "diffR" and "regimeR" now shows componentwise test results BUGFIXES o Removing MAKEFLAG "-D_GLIBCXX_PARALLEL" because it is experimental CHANGES IN VERSION 0.99.4 ------------------------- BUGFIXES o Removing PKG_CPPFLAGS and PKG_LIBS variables from src/Makevars CHANGES IN VERSION 0.99.3 ------------------------- BUGFIXES o Fixing imports in roxygen2 CHANGES IN VERSION 0.99.2 ------------------------- FEATURES o Vignette finished o Documentation for NormRFit-class & NormRCountConfig-class updated BUGFIXES o deploy.log removed CHANGES IN VERSION 0.99.1 ------------------------- FEATURES o Added examples for normr-methods, BamCountConfig-class & NormRFit-class o Moved all documentation to one manpage (normr.Rd) o Vignette: knitr-based vignette for normr finished o exportR(): Export NormRFit objects to bed, bedGraph and bigWig o plot(): Produce a small diagnostic plot for NormRFit objects o diffR(): Intersection of results for switched labels increases specificity BUGFIXES o Removed deploy.log o Fixed build errors and warnings o Fixed failing test CHANGES IN VERSION 0.99.0 ------------------------- FEATURES o huge performance speedup by data compression to unique tupels only o Kahan summation for log posterior summation to reduce numerical error o Standardized enrichment computation in C++. This enrichment can be well compared between various ChIP-seq experiments o exportR() function provides methods to export results of fits as a region bed file or bigWig track of standardized enrichment