NEWS

---

ASpli 2.11.1

BUG FIXES

• Solve bug in readCounts. Undefined seqnames produced invalid junctions.orders
• Change package mantainer

ASpli 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.

ASpli 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.

ASpli 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.

ASpli 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

ASpli 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.

ASpli 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.

ASpli 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.

ASpli 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.

ASpli 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.

ASpli 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.

ASpli 1.3.9

BUG FIXES

• plotBins function now shows x-tick labels correctly.

ASpli 1.3.8

FEATURES

• PlotGenomicRegions do not requires an ASpliCounts object

BUG FIXES

• AsDiscover and DUreport can handle conditions with one samples. Results should be taken with care, but ASpli doesn't break.

ASpli 1.3.7

FEATURES

• Added functions to filter elements in ASpliCounts objects by read counts and read density.

ASpli 1.3.6

FEATURES

• geneMode is the default mode of offset estimation.

ASpli 1.2.1

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).

ASpli 1.1.0

NEW FEATURES

• New ASpli_binGenome.log file. It reports the number of features being processed

ASpli 0.98

NEW FEATURES

• Multiple bins are reclassified using annotated junctions