Installation

Table of Contents

dNdS-Fun is implemented as an R package, which can be installed from GitHub by:

Installation #

Install as an R Package #

Requirements:R version > 4.0.5
To install dNdS-Fun from GitHub using devtools, run the following commands in R:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("jianyanglab/dNdS-Fun", build_vignettes = FALSE)

Install from Source Code #

Requirements:

  1. parallel (version >= 4.0.5)
  2. data.table (version >= 1.16.4)
  3. MASS (version >= 7.3.56)
  4. doParallel (version >= 1.0.17)
  5. foreach (version >= 1.5.2)
  6. GenomicRanges (install via Bioconductor, version >= 1.42.0)
  7. Biostrings (install via Bioconductor, version >= 2.58.0)
  8. tabix (command-line tool, version >= 0.2.6)

Installation Steps: #

  1. Install necessary R packages: 
     # Install Bioconductor manager if not already installed     
 if (!requireNamespace("BiocManager", quietly = TRUE))    
      install.packages("BiocManager")   

 # Install required CRAN packages    
 install.packages(c("parallel", "data.table", "MASS", "doParallel", "foreach"))   

 # Install required Bioconductor packages     
 BiocManager::install(c("GenomicRanges", "Biostrings"))
  2. Install tabix:
    • On Linux: Use your package manager, e.g., sudo apt-get install tabix.
    • On macOS: Use Homebrew, e.g., brew install htslib.
    • On Windows: Precompiled binaries are available; ensure tabix is added to your system PATH.
  3. Clone the dNdS-Fun repository and install:
    bash 
    git clone https://github.com/jianyanglab/dNdS-Fun.git

    Then, from within R:

    setwd("path_to_dNdS-Fun")   
install.packages(".", repos = NULL, type = "source")