limorhyde2

limorhyde2 is an approach to analyze rhythmic, genome-scale data in a way that focuses on effect sizes. For a detailed description of limorhyde2 along with examples showing its utility on data from one or more conditions, check out the preprint.

Installation

If you use RStudio, go to Tools -> Global Options… -> Packages -> Add… (under Secondary repositories), then enter:

You only have to do this once. Then you can install or update the package by entering:

if (!requireNamespace('remotes', quietly = TRUE))
  install.packages('remotes')
remotes::install_github('stephens999/ashr')

if (!requireNamespace('BiocManager', quietly = TRUE))
  install.packages('BiocManager')
BiocManager::install('limorhyde2')

Alternatively, you can install or update the package by entering:

if (!requireNamespace('remotes', quietly = TRUE))
  install.packages('remotes')
remotes::install_github('stephens999/ashr')

if (!requireNamespace('BiocManager', quietly = TRUE))
  install.packages('BiocManager')
BiocManager::install('limorhyde2', site_repository = 'https://hugheylab.github.io/drat/')

There’s also a docker image, which has all dependencies installed.

docker pull hugheylab/hugheyverse

Usage

See the examples and detailed guidance in the reference documentation.