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Welcome to the SCAPE wiki

SCAPE (Single Cell Alternative Polyadenylation using Expectation-maximization) is a tool to explore alternative polyadenylation at single cell level based 3'-tag sequencing data.

Getting Started

• Getting Started with SCAPE

  • Tutorial

• Analysis APA in R

  • Brain and bone marrow
  • mouse HSC

SCAPE models the scRNA-seq data as a mixture of K isoform components and one noise component, i.e. a read either comes from an isoform or belongs to noise. The i th (i = 1…K) isoform component (Fig. 1) has three parameters: (a) the mean position of the pA site α_i, (b) the standard deviation (std) of the pA site β_i, (c) the weight or proportion π_i. The number of components is automatically selected using Bayesian Information Criterion (BIC). We use the Expectation-Maximization (EM) algorithm and numerical optimization to infer the parameters.

For questions regarding the usage of SCAPE use the issues section.