https://github.com/lmweber/regsplice

R package for detection of differential exon usage in RNA-seq and exon microarray data
https://github.com/lmweber/regsplice

Last synced: 11 days ago
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R package for detection of differential exon usage in RNA-seq and exon microarray data

• Host: GitHub
• URL: https://github.com/lmweber/regsplice
• Owner: lmweber
• License: mit
• Created: 2015-07-30T16:21:26.000Z (over 9 years ago)
• Default Branch: devel
• Last Pushed: 2024-03-17T18:39:08.000Z (8 months ago)
• Last Synced: 2024-10-11T22:26:34.494Z (28 days ago)
• Language: R
• Homepage:
• Size: 14.2 MB
• Stars: 3
• Watchers: 4
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# regsplice

[![Travis-CI Build Status](https://travis-ci.org/lmweber/regsplice.svg?branch=master)](https://travis-ci.org/lmweber/regsplice)

[![codecov](https://codecov.io/gh/lmweber/regsplice/branch/master/graph/badge.svg)](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"))

```