Differential Splicing

• cufflinks
• dexSeq

• junctionSeq

• LeafCutter (Li, Y. I., Knowles, D. A., Humphrey, J., Barbeira, A. N., Dickinson, S. P., Im, H. K., & Pritchard, J. K. (2016). LeafCutter: Annotation-free quantification of RNA splicing. bioRxiv)