NEWS

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eisaR 1.25.1

• Rewrite plotEISA to use ggplot2 (and return a ggplot object), set the aspect ratio of the plot to 1 and add an identity line. Additional arguments provided via ..., previously passed to plot(), are ignored.

eisaR 1.21.1

• Various code improvements detected by lintr

eisaR 1.15.1

• Add legacyQLF argument to runEISA (will be passed to edgeR::glmQLFit)

eisaR 1.5.2

• Add options to collapse introns by gene and restrict introns to feature ranges in getFeatureRanges.

eisaR 1.0

• Initial version
• R implementation of Exon-Intron Split Analysis (EISA, doi: 10.1038/nbt.3269)
• functionality for extracting spliced and unspliced transcript sequences, as well as intron sequences. e.g. for use in RNA velocity analysis