QCumber --> Qllelic
Name changed to avoid confusion with an existing package for sequencing QC.
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 current version of this package in R:
devtools::install_github("gimelbrantlab/QCumber")Installation takes less than 1 minute. To install a specific version: devtools::install_github("gimelbrantlab/[email protected]")
Full documentation: pdf document.
Please see walk-through examples on the Wiki page
Please report bugs to the Github issues page.