Qllelic is a set of R tools for quantification of allele-specific expression. It relies on two or more technical replicate RNA-seq libraries to calculate Quality Correction Constant (QCC) and use it to correct for allelic imbalance overdipserion. Qllelic analysis starts with a table of allelic counts per gene, calculated from RNA-seq data using any analysis pipeline such as ASEReadCounter*.
Mendelevich A.*, Vinogradova S.*, Gupta S., Mironov A., Sunyaev S., Gimelbrant A. "Replicate sequencing libraries are important for quantification of allelic imbalance", Nat Commun 12, 3370 (2021). https://doi.org/10.1038/s41467-021-23544-8
To install current version of this package in R:
devtools::install_github("gimelbrantlab/Qllelic")Installation takes less than 1 minute.
To install a previous version: devtools::install_github("gimelbrantlab/Qllelic@v0.3.1"), please take into account that it existed with different name, so it would be installed as "QCumber".
Full documentation: pdf document.
Please see walk-through examples on the Wiki page
Please report bugs to the Github issues page.