CHANGES IN VERSION 1.5.1 ------------------------- BUG FIXES * readCounts supports identical gene names in different chromosomes. * Fixed default value for minAnchor argument of readCounts code, man page and vignette. CHANGES IN VERSION 1.3.12 ------------------------- FEATURES * Events named previously as 'as' are now names 'Undefined AS' for the sake of clarity. * Enhancement to the vignettes. BUG FIXES * Added verbose and filterWithContrasted arguments to DUreport method. CHANGES IN VERSION 1.3.11 ------------------------- FEATURES * Change the assigning of some 'ES*' events to 'as' events. * Added verbose option of DUreportBinSplice method * junctionDUReport methods changed to junctionDUreport to be consistent with other methods names. BUG FIXES * Many corrections in the vignette and man pages. * ZNF410_E013.gr.pdf file in vignettes/images was changed to ZNF410_E013_gr.pdf to be correctly used in the latex code. CHANGES IN VERSION 1.3.10 ------------------------- DOCUMENTATION * Vignette is updated to reflect changes in objects, methods and functions. Minor revisions are still required. BUG FIXES * PlotGenomicRegions now can make plots from unmerged bams correctly. CHANGES IN VERSION 1.3.9 ------------------------ BUG FIXES * plotBins function now shows x-tick labels correctly. CHANGES IN VERSION 1.3.8 ------------------------ FEATURES * PlotGenomicRegions do not requires an ASpliCounts object CHANGES IN VERSION 1.3.8 ------------------------ BUG FIXES * AsDiscover and DUreport can handle conditions with one samples. Results should be taken with care, but ASpli doesn't break. CHANGES IN VERSION 1.3.7 ------------------------ FEATURES * Added functions to filter elements in ASpliCounts objects by read counts and read density. CHANGES IN VERSION 1.3.6 ------------------------ FEATURES * geneMode is the default mode of offset estimation. CHANGES IN VERSION 1.2.1 / 1.3.1 ------------------------ BUG FIXES * AsDiscover() no longer contains mixed row data for some IR and IR* bins in irPIR table. * DUReport() calculates correctly junction ratio for junctions sharing their end in junction.counts table. * DUReport() no longer fails when there are no junctions that share their start or end. * reacCounts() requires an explicit targets argument, instead of taking it from the global environment (in which may not exist with that name). CHANGES IN VERSION 1.1.0 ------------------------ NEW FEATURES * New ASpli_binGenome.log file. It reports the number of features being processed CHANGES IN VERSION 0.98 ------------------------- NEW FEATURES * Multiple bins are reclassified using annotated junctions