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# regsplice [![Travis-CI Build Status](]( [![codecov](]( This repository contains the development version of the R package `regsplice`. The release version is available from [Bioconductor]( 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]( 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]( 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]( - `limma`, `edgeR`, `SummarizedExperiment` (from [Bioconductor]( 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")) ```