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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, please wait for the preprint.

Installation

Option 1: CRAN

if (!requireNamespace('BiocManager', quietly = TRUE))
  install.packages('BiocManager')
BiocManager::install(c('DESeq2', 'limma'))
install.packages('limorhyde2')

Option 2: Hughey Lab Drat Repository

  1. Install BiocManager.

    if (!requireNamespace('BiocManager', quietly = TRUE))
      install.packages('BiocManager')
  2. 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:

    BiocManager::install('limorhyde2')

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

    BiocManager::install('limorhyde2', site_repository = 'https://hugheylab.github.io/drat/')

Usage

See the examples and detailed guidance in the reference documentation.