<!-- README.md is generated from README.Rmd. Please edit that file --> # `dearseq` <a><img src='man/figures/logo.svg' align="right" height="139" /></a> <!-- [](https://cran.r-project.org/package=dearseq) --> [](https://travis-ci.org/borishejblum/dearseq) [](https://ci.appveyor.com/project/borishejblum/dearseq) [](https://codecov.io/github/borishejblum/dearseq?branch=master) <!-- [](https://www.r-pkg.org/pkg/dearseq) --> ## Overview `dearseq` is a package for analyzing RNA-seq data. The 2 main functions of the package are `dear_seq()` and `dgsa_seq()`: - **Gene-wise Differential Analysis of RNA-seq data** can be performed using the function `dear_seq()`. - **Gene Set Analysis of RNA-seq data** can be performed using the function `dgsa_seq()`. The methods implemented in this package are detailed in the following articles: > Gauthier M, Agniel D, Thiébaut R & Hejblum BP (2019). dearseq: a > variance component score test for RNA-Seq differential analysis that > effectively controls the false discovery rate, *bioRxiv* 635714. > [DOI: 10.1101/635714](https://doi.org/10.1101/635714) > Agniel D & Hejblum BP (2017). Variance component score test for > time-course gene set analysis of longitudinal RNA-seq data, > [*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 ***`dearseq` is currently [under review](https://github.com/Bioconductor/Contributions/issues/1307) to be included in [Bioconductor](http://www.bioconductor.org)*** Meanwhile, the easiest way to get `dearseq` is to install its development version from the `dev` branch on [GitHub](https://github.com/borishejblum/dearseq): ``` r #install.packages("devtools") devtools::install_github("borishejblum/dearseq", ref="dev") ``` – Marine Gauthier, Denis Agniel & Boris Hejblum