README.Rmd

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output: github_document
---

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```{r, echo = FALSE}
knitr::opts_chunk$set(
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# `tcgsaseq`

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## Overview

`tcgsaseq` is a package for analyzing RNA-seq data. The 2 main functions of the package are `varseq` and `tcgsa_seq`: 

* **Gene-wise Differential Analysis of RNA-seq data** can be performed using the function `varseq`. 
* **Gene Set Analysis of RNA-seq data** can be performed using the function `tcgsa_seq`. 

The method implemented in this package is detailed in the following article:

> Agniel D & Hejblum BP (2017). Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, 2017, [*Biostatistics*](https://academic.oup.com/biostatistics/article-abstract/18/4/589/3065599), 18(4):589-604. [arXiv:1605.02351](https://arxiv.org/abs/1605.02351v4) [DOI: 10.1093/biostatistics/kxx005](https://doi.org/10.1093/biostatistics/kxx005)


## Installation


The easiest way to get `tcgsaseq` is to install it from [CRAN](https://cran.r-project.org/package=tcgsaseq):
```{r CRAN-install, eval=FALSE}
install.packages("tcgsaseq")
```

Or to get the development version from [GitHub](https://github.com/denisagniel/tcgsaseq):
```{r GitHub-install, eval=FALSE}
#install.packages("devtools")
devtools::install_github("denisagniel/tcgsaseq")
```

 -- Denis Agniel and Boris Hejblum