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

Installation

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/QCumber@v0.3.1")

Manual

Full documentation: pdf document.

Please see walk-through examples on the Wiki page

• for QCC calculation and CI estimation
• for AI differential analysis for two samples

Reporting bugs

Please report bugs to the Github issues page.

License

GNU General Public License v3.0