CHANGES IN VERSION 2.11.1 ------------------------ BUG FIXES * Solve bug in readCounts. Undefined seqnames produced invalid junctions.orders * Change package mantainer CHANGES IN VERSION 2.10.1 ------------------------ BUG FIXES * Solves jCounts() Error in av[at] <- a[at] : NAs are not allowed in subscripted assignments bug with large junction possitions. CHANGES IN VERSION 2.3.1 ------------------------ BUG FIXES * Function vecMin inside .filterJunctionBySample threw an error if every element in counts vector was larger than the filter. Now works correctly using pmin instead. CHANGES IN VERSION 2.1.3 ------------------------- NEW CITATION * ASpli was published on Bioinformatics * https://doi.org/10.1093/bioinformatics/btab141 FEATURES * binGenome now displays a progress bar when binning. BUG FIXES * gbCounts identifies correctly NA in junction's name * minAnchor in jCounts was hardcoded so it had no impact on analysis. It is being passed correctly now. CHANGES IN VERSION 2.1 ------------------------- NEW FUNCTIONS AND FUNCTIONALITIES * New locus plot helper function .plotGenePattern. * plots coverage, junctions and architecture FEATURES * Enhancement to the vignettes. * Quick start section was modify in order to use gtf and bam files provided by ASpli package * Add new section ASpli overview in vignette BUG FIXES * binGenome function assigns correctly bins located at the start and the end of each gene * binGenome function calculates correctly gene range overlap CHANGES IN VERSION 1.99.3 ------------------------- NEW FUNCTIONS AND FUNCTIONALITIES * New parameters for gbCounts and jCounts functions: * libType: to specify single end ("SE") or paired end ("PE") library * strandMode: - 0: strand of the pair is always *. - 1: strand of the pair is strand of its first alignment - 2: strand of the pair is strand of its last alignment. CHANGES IN VERSION 1.99.1 ------------------------- NEW FUNCTIONS AND FUNCTIONALITIES * For counting: gbCounts and jCounts. We add library type and strand-specificity parameters. * For DU estimation: DUreport.norm and DUreport.offset * For prepare DU reports: filterSignals, gbDUreport, integrateSignals, jDUreport, splicingReport and junctionsPJU * For printing reports: exportIntegratedSignals, writeJDU and writeSplicingReport FUNCTIONS DEPRECATED * loadBAM: will be replaced by gbCounts. Bams files are proccesed one by one, according target object. It improves running time and memory usage * readCounts: it is replaced by gbCounts * AsDiscover: it is replaced by jCounts * DUreport: it is replaced by gbDUreport and jDUreport * mergeBinDUAS: has no direct replacement. * plotGenomicRegions: has not direct replacement. There are new functions for exportiing results into HTML pages. 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