S-YIN/FFPEnorm: FFPE RNA-Seq Normalization

FFPEnorm provides two normalization methods, MIXnorm and SMIXnorm, developed for Formalin-Fixed Paraffin-Embedded (FFPE) tissues RNA-seq data. MIXnorm is based on a two-component mixture model. Expressed genes are modeled by truncated normal distributions (in natural log scale). Non-expressed genes are modeled by zero-inflated Poisson distributions. SMIXnorm is a simplified version of MIXnorm. The performance of SMIXnorm is comparable to MIXnorm, while requiring less computing effort. Compared to MIXnorm, the simplifications are: 1.Expressed genes are modeled by normal distributions without truncation; 2. Non-expressed genes are modeled by zero-inflated Poisson distributions with common Poisson mean. Note that though designed for FFPE RNA-seq data, MIXnorm and SMIXnorm are directly applicable to fresh frozen or like sample RNA-seq data.

Getting started

Package details

Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
S-YIN/FFPEnorm documentation built on Nov. 20, 2019, 7:05 a.m.