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: firstname.lastname@example.org.Download and Run
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
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
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.