README.md

In gimelbrantlab/QCumber: Detects differential allelic imbalance from RNA-seq data

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

gimelbrantlab/QCumber documentation built on Feb. 26, 2020, 6:17 p.m.