limorhyde (linear models for rhythmicity, design) 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.
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.
You only have to do this once.
Alternatively, enter the following command each time you want to install or update the package.
Now you can install the package.
install.packages('limorhyde', type = 'source')
You can update the package using update.packages().
There’s also docker image, which has all dependencies installed.
For an introduction to the package, read the vignette. For more details, check out the reference documentation.