README.md

In jingwyang/TreeExp: the R package for analyzing expression evolution based on RNA-seq data

title: "README" author: "Jingwen Yang" date: "2019/4/27" output: md_document

TreeExp

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:

{r, eval=FALSE} install.packages('devtools') devtools::install_github("jingwyang/TreeExp")

Please refer to Tutorial for startup guide of TreeExp.

jingwyang/TreeExp documentation built on June 11, 2019, 6:17 p.m.