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QCumber 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. QCumber 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. "Unexpected variability of allelic imbalance estimates from RNA sequencing". bioRxiv link
To install this package in R:
devtools::install_github("gimelbrantlab/QCumber")Please see worked examples in this wiki.
You may also use ?function notation for help.