*(a) IsoDOT work flow. The dash line indicates that known isoform annotation (i.e., transcriptome annotation) is optional, (b) A gene with 3 exons and 3 possible isoforms. (c) A matrix of input data. Each row corresponding to an exon set. The column “Count” is the number of RNA-seq fragments at each exon set, and the columns “isoform k” for k = 1,2,3 give the effective lengths of each exon set within each isoform, and specifically, η _{A,k} is the effective length of exon set A for the k-th isoform. NB(μ,φ) indicates a negative binomial distribution with mean μ, and dispersion parameter φ.*

**Availability** – An R package of IsoDOT is available at http://www.bios.unc.edu/∼weisun/software/isoform.htm.

Sun W, Liu Y, Crowley JJ, Chen TH, Zhou H, Chu H, Huang S, Kuan PF, Li Y, Miller DR, Shaw GD, Wu Y, Zhabotynsky V, McMillan L, Zou F, Sullivan PF, de Villena FP. (2015) **IsoDOT Detects Differential RNA-isoform Expression/Usage with respect to a Categorical or Continuous Covariate with High Sensitivity and Specificity**. *J Am Stat Assoc* 110(511):975-986. [article]

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