--- title: "Getting started" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Getting started} %\VignetteEngine{knitr::rmarkdown} ---





# 1. Install **myTAI**

```{r, echo = FALSE, message = FALSE} library(myTAI) knitr::opts_chunk$set( comment = "#>", error = FALSE, tidy = FALSE, width = 750) ``` ```R # from CRAN install.packages("myTAI", dependencies = TRUE) # or, the developer version containing the newest features devtools::install_github("drostlab/myTAI") # make sure myTAI version is > 2.0.0 packageVersion("myTAI") ```



# 2. Run **myTAI**

```{r message = FALSE, results = FALSE, fig.height=4, fig.width=6, fig.alt="plot_signature function output", dev.args = list(bg = 'transparent'), fig.align='center'} library(myTAI) # obtain an example phylo-expression object data("example_phyex_set") # plot away! myTAI::plot_signature(example_phyex_set) ```

or with [your `BulkPhyloExpressionSet` dataset](phylo-expression-object.html).

PhyEx overview





# 3. Enjoy 🍹

(and don't forget to [cite](https://doi.org/10.1093/bioinformatics/btx835))









Want to use myTAI on your data? → click on the icons 🧚 below.

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[📊](phylo-expression-object.html) Bring your datasets into myTAI. [📈](tai-stats.html) Statistical analyses → learn about our permutation tests. [🛡️](tai-transform.html) Check the robustness of your patterns. [🔨](tai-breaker.html) Destroy the hourglass! → `gaTAI` functions to extract the genes that drive your evolutionary transcriptomic patterns. [📚](phylostratigraphy.html) Read about gene age inference (phylostratigraphy) and transcriptome age index. [🌄](tai-gallery.html) Check out our gallery of example plots + functions.

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Want to learn even more? → check out our vignettes under the [`Articles`](index.html) tab or the [`Reference`](../reference/index.html) tab for a list of functions and their documentation.