CHANGES IN VERSION 1.10.0 ------------------------ o Bug fixes and documentation improvements CHANGES IN VERSION 1.8.0 ------------------------ o Bug fixes and other improvements CHANGES IN VERSION 1.6.0 ------------------------ o New vignette o Changes in the SGVariants and SGVariantCounts class. Instances created with previous versions of SGSeq have to be updated. o Replaced functions for accessing assay data with two generic functions counts() and FPKM() o Support BamFileLists in sample info o Changed behavior of the annotate() function when assigning gene names o Changed behavior of the min_denominator argument in analyzeVariants() and getSGVariantCounts(). The specfied minimum count now has to be achieved at either the start or end of the event. o Adjacent exons no longer cause a warning in convertToTxFeatures() o Deprecated legacy classes TxVariants, TxVariantCounts o Bug fixes and other improvements CHANGES IN VERSION 1.4.0 ------------------------ o Added importTranscripts() for importing annotation from GFF format o Added plotCoverage() for visualization of per-base read coverage and junction read counts o Added predictVariantEffects() for predicting the effect of splice variants on annotated protein-coding transcripts o findSGVariants() is now able to deal with more complex gene models o SGVariants columns closed5p and closed3p now refer to individual splice variants rather than the splice event they belong to o Bug fixes and other improvements CHANGES IN VERSION 1.2.0 ------------------------ o Renamed class TxVariants to SGVariants o Renamed class TxVariantCounts to SGVariantCounts o Renamed findTxVariants() to findSGVariants() o Renamed getTxVariantCounts() to getSGVariantCounts() o Parallelization is now controlled with a single cores argument o Argument max_complexity for predictTxFeatures() controls skipping of problematic regions o getBamInfo() is no longer run as part of analyzeFeatures() o getSGVariantCounts() now supports obtaining counts from BAM files o Bug fixes and other improvements