# regsplice
[](https://travis-ci.org/lmweber/regsplice)
[](https://codecov.io/gh/lmweber/regsplice)
This repository contains the development version of the R package `regsplice`.
The release version is available from [Bioconductor](https://bioconductor.org/packages/regsplice/).
The `regsplice` package implements statistical methods for the detection of differential exon usage (differential splicing) in RNA sequencing (RNA-seq) and exon microarray data sets. The `regsplice` methods are based on the use of the lasso (L1-regularization) to improve the power of standard generalized linear models. A key advantage is that runtimes are fast compared to other leading approaches.
A paper describing the statistical methodology and performance comparisons with other methods is currently in preparation.
## Install release version
The release version can be installed from [Bioconductor](https://bioconductor.org/packages/regsplice/) using the Bioconductor installer. This will also install all required dependencies. This is the recommended option for most users.
```{r}
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("regsplice")
```
## Install development version
The development version can be installed from this GitHub repository using `devtools::install_github`.
```{r}
install.packages("devtools")
library(devtools)
install_github("lmweber/regsplice")
```
Alternatively, the development version can also be installed using the "Devel" version of Bioconductor (see [Bioconductor documentation](http://bioconductor.org/developers/how-to/useDevel/) for details). However, the Bioconductor Devel version may sometimes be a few days behind the GitHub version.
## Dependencies
The `regsplice` package depends on:
- `glmnet`, `pbapply` (from [CRAN](https://cran.r-project.org/))
- `limma`, `edgeR`, `SummarizedExperiment` (from [Bioconductor](http://bioconductor.org/))
If you install using the Bioconductor installer, all dependencies will be installed automatically.
If you install from GitHub, the Bioconductor dependencies need to be installed separately.
```{r}
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install(c("limma", "edgeR", "SummarizedExperiment"))
```
