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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# `tcgsaseq`
[](https://cran.r-project.org/package=tcgsaseq)
[](https://travis-ci.org/denisagniel/tcgsaseq)
[](https://ci.appveyor.com/project/denisagniel/tcgsaseq)
[](https://coveralls.io/r/denisagniel/tcgsaseq)
[](https://www.r-pkg.org/pkg/tcgsaseq)
<img src="man/figures/lifecycle-soft-deprecated.svg" width="17%" />
## WARNING: soft-deprecation
`tcgsaseq` capabilities and features have been incorporated into the [`Bioconductor` package `dearseq`](https://bioconductor.org/packages/release/bioc/html/dearseq.html).
`tcgsaseq` will be kept as the legacy companion package of the 2017 Agniel & Hejblum [*Biostatistics*](https://academic.oup.com/biostatistics/article-abstract/18/4/589/3065599) article, but will not be further developped or extended.
If you are interested in using tcgsaseq, you should probably rather look into the newer and more comprehensive `dearseq` package.
## Overview
`tcgsaseq` is a package for analyzing RNA-seq data. The 2 main functions of the package are `varcompseq` and `tcgsa_seq`:
* **Gene-wise Differential Analysis of RNA-seq data** can be performed using the function `varcompseq`.
* **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