CHANGES IN VERSION 1.1.7 ------------------------ NEW FEATURES o Users can now control 'output_format' and 'clean' options from rmarkdown::render() when running derfinderReport() CHANGES IN VERSION 1.1.3 ------------------------ BUG FIXES o Adapted derfinderReport() to derfinder 1.1.5 CHANGES IN VERSION 0.99.0 ------------------------- NEW FEATURES o Preparing to submit to Bioconductor. SIGNIFICANT USER-VISIBLE CHANGES o Updated the vignette and the package to work with recent versions of the packages this package depends on. o Renamed the package from derfinderReport to regionReport and generateReport() to derfinderReport(). In the future we will add another report for a general GRanges object. o Simplified derfinderReport()'s call by using advanced arguments. o Added Travis integration. CHANGES IN VERSION 0.0.18 ------------------------- o Now derfinderReport() has a 'chrsStyle' argument to match changes in derfinder version 0.0.60. 'chrsStyle' is set to 'UCSC' by default. CHANGES IN VERSION 0.0.17 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Made more robust for cases where there is a small number of significant DERs: need at least 3 observations by chr for the chr to be included in the density plots. CHANGES IN VERSION 0.0.16 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o MA-style plots now use the scaling factor. o Using a GAM smoother instead of loess for MA-style plots. Helps for cases with many regions. CHANGES IN VERSION 0.0.13 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Added a vignette CHANGES IN VERSION 0.0.12 ------------------------- BUG FIXES o complying with BiocCheck version 1.0.0 CHANGES IN VERSION 0.0.11 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o genomicState data moved to derfinder 0.0.53 CHANGES IN VERSION 0.0.8 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Now requires knitrBootstrap 1.0.0 o Matches derfinder version 0.0.49 CHANGES IN VERSION 0.0.3 ------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Matches derfinder version 0.0.34 CHANGES IN VERSION 0.0.1 ----------------------- NEW FEATURES o Migrated from derfinder