ISoLDE (version 1.0.2)

ISoLDE-package: INTEGRATIVE STATISTICS OF ALLELE DEPENDENT EXPRESSION

Description

This package provides a new method for identifying genes with allelic bias. This method is dedicated to data arising from RNA sequencing technologies. The ISoLDE package implements original statistical methodology described in the publication below.

Details

ISoLDE method has been motivated by several literature limitations in taking into account the data specificities and in making the most of biological replicates. It is based on the definition of a new criterion using robust estimation of the data variability. Variability estimation is of high importance in statistical testing procedures because a difference significance can only be assessed with regards to the intrinsic data variability.

Two methods are available to identify allele specific expression: one is based on bootstrap resampling while the second one uses an empirical threshold. The first one is much more satisfying and is likely to give the most reliable results but it can only be applied to data with at least three biological replicates for each reciprocal cross. While strongly recommending to use at least three replicates, the second method implements a robust solution when only two replicates are available.

References

Reynès, C. et al. (2016): ISoLDE: a new method for identification of allelic imbalance. Submitted