TreeExp is an R package developed to provides useful phylogenetic tools applicable to RNA-seq data. The package can be applied to comparative expression evolution analysis, which includes but not liminited to:
- pairwise expression distance estimation;
- relative rate test for transcriptome evolution;
- the strength of expression conservation estimation;
- ancestral transcriptome inference.
Statistical methods implemented in the package was based on Ornstein-Uhlenbeck (OU) model of transcriptome evolution which claims that expression changes are constrained by stabilizing selection.
TreeExp package is under active developing, current developing version 2.0 is available at https://github.com/jingwyang/TreeExp.
A convenient way to install package from github is through devtools package:
Please refer to Tutorial for startup guide of TreeExp.