TreeExp is an R package that performs analyses of expression evolution from RNA-seq data, including optimized input formatting, normalization and pair-wise distance evaluation, expression character tree inference and preliminary phylogenetic network analysis.
TreeExp package 2.0 is published at Bioinformatics: https://doi.org/10.1093/bioinformatics/btz405
A convenient way to install package from github is through devtools package:
install.packages('devtools')
devtools::install_github("hr1912/TreeExp")
Users can also download TreeExp package and install locally through:
install.packages("filePath/TreeExp.2.0.tar.gz", repos = NUll, type = "source")
Please refer to vignettes for startup guide of TreeExp.
A more detailed usage guide by Jingwen Yang is availiable at: https://jingwyang.github.io/TreeExp-Tutorial/