README.md

In hugheylab/limorhyde2: Quantify Rhythmicity and Differential Rhythmicity in Genomic Data

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 for transcriptome data, please check out the paper.

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.

   r 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:

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

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

   r BiocManager::install('limorhyde2')

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

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

Usage

See the examples and detailed guidance in the reference documentation.

hugheylab/limorhyde2 documentation built on Jan. 29, 2024, 8:36 p.m.