HMMASE

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.

Contact: hengwang@msu.edu.

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 "HMMASE_1.0.zip".

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

install.packages("HMMASE_1.0.tar.gz",repos=NULL,type="source").

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

install.packages("HMMASE_1.0.tar.gz",repos=NULL,type="source").


Documentation

User Manual
Algorithm Details


Citation

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.