Summary: A package that analyzes SNP and allele-specific read counts from RNAseq data to infer genotypes and to assess ASE.

Platforms: Linux, Mac, Windows.

Requirements: R 3.0.

Authors: Juan P. Steibel, Heng Wang and Ping-Shou Zhong.


Download and Run

Windows version
Mac version
Linux version

How To Install

Note that the package has to be installed under R with version 3.00 and above.

In Windows version R, please click on packages and choose "install package(s) from local zip file ...". Then select the file "".

To install in Mac version R, first save the package "HMMASE_1.0.tar.gz" into a local folder and change the working dircetory in R to that folder. Then use the following command to install the package


To install in Linux version R, first save linux version R package "HMMASE_1.0.tar.gz" into a folder and change the dircetory to that folder. If the R package R.utils was not installed in your linux system, you might need to install R.utils before installing the package R HMMASE. Then open R and use the following command to install the package in R



User Manual
Algorithm Details


Juan P. Steibel, Heng Wang and Ping-Shou Zhong (2013). A Hidden Markov Approach for Ascertaining cSNP Genotypes from RNA Sequence Data in the Presence of Allelic Imbalance by Exploiting Linkage Disequilibrium , To appear in BMC Bioinformatics.