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