• MISO (Mixture of Isoforms) - MISO is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. By modeling the generative process by which reads are produced from isoforms in RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.

    MISO treats the expression level of a set of isoforms as a random variable and estimates a distribution over the values of this variable. The estimation algorithm is based on sampling, and falls in the family of techniques known as Markov Chain Monte Carlo (“MCMC”).

  • sashimi-plot - sashimi-plot is a utility for visualizing RNA-Seq reads in multiple experimental samples along gene models and for plotting MISO estimates. In particular, it can: (1) plot raw RNA-Seq densities along exons and junctions for multiple samples, while simultaneously visualizing the gene model/isoforms to which reads map, and (2) plot MISO output alongside the raw data (or separately) as well as the insert length distribution or other summary statistics related to RNA-Seq samples.