biplabendu / limorhyde

LimoRhyde R package

limorhyde

limorhyde (linear models for rhythmicity, design) is an R package that enables differential analysis of circadian transcriptome data using state-of-the-art methods for differential expression.

For details about the method and to see how we used it to analyze circadian transcriptome data from various experimental designs, check out the paper and the accompanying results.

Installation

First add the hugheylab repository to your repos. There are multiple ways to do this.

If you use RStudio, go to Tools -> Global Options... -> Packages -> Add... (under Secondary repositories), then enter the following values.

• Name: hugheylab
• Url: https://hugheylab.github.io/drat/

You only have to do this once.

Alternatively, you can enter the following command each time you want to install or update the package.

options(repos = c(getOption('repos'), 'https://hugheylab.github.io/drat/'))

Now you can install the package.

install.packages('limorhyde', type = 'source')

You can update the package using update.packages().

Docker

You can also use a pre-built docker image, which has all dependencies installed.

docker pull hugheylab/hugheyverse

Getting started

See the vignette and the documentation.

browseVignettes('limorhyde')
?limorhyde::limorhyde