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Obsolete (replaced with renamed version Qllelic, due to naming conflict with already existing QCumber software)
QCumber is a set of R tools for quantification of allelic imbalance and differential allele-specific expression. For each sample, QCumber compares data from two or more technical replicate RNA-seq libraries to calculate Quality Correction Constant (QCC) and then uses it to correct for allelic imbalance overdispersion. QCumber analysis starts with a table of allelic counts per gene, calculated from RNA-seq data using any analysis pipeline such as ASEReadCounter*.
To install this package in R: devtools::install_github("gimelbrantlab/QCumber")
For quick start, see walk-throughs:
- allelic imbalance calculation for one sample;
- differential allelic imbalance for two samples.
For detailed information see documentation. For context help in R session, you can use ?function notation.
For software dependencies see the corresponding wiki page.
Detailed description of statistical analysis implemented in QCumber can be found in: Mendelevich A.*, Vinogradova S.*, Gupta S., Mironov A., Sunyaev S., Gimelbrant A. "Unexpected variability of allelic imbalance estimates from RNA sequencing". bioRxiv link
