kfwins2022/deltarpkm

An R package for a rapid differential gene presence analysis between similar genomes

deltaRpkm

An R package for a rapid differential gene presence analysis between large datasets of similar bacterial genomes

Background

deltaRpkm is an R package whose main purpose is to quickly identify genes potentially involved in a given trait by performing a differential analysis of genes coverage between two sets of closely related bacterial genomes.
The package provides functions to compute the RPKM, the deltaRPKM, identify candidate genes filtering and make heatmap plots.
It also includes methods to perform some batch effects controls and diagnostics plots.

Install

Download (from the deltaRpkm/bin repo) the binary file that is specific to your system:

deltaRpkm_0.1.0_R_x86_64-pc-linux-gnu.tar.gz      # Ubuntu (18 LTS)
deltaRpkm_0.1.0_mac.tgz                           # MacOS (10.13)  
deltaRpkm_0.1.0.zip                               # Windows

and then, on a terminal on your local working directory:

# install the package on your system, from the terminal:  
R CMD INSTALL path/2/deltaRpkm_0.1.0_R_x86_64-pc-linux-gnu.tar.gz

Note that any missing CRAN or Bioconductor packages required by deltaRpkm need to be installed accordingly.

Alternatively, it can be installed from inside R/RStudio as:

> install.packages("path/2/deltaRpkm_0.1.0_R_x86_64-pc-linux-gnu.tar.gz", repos = NULL, dependencies = TRUE)

This will install any missing CRAN R packages required by deltaRpkm. But missing Bioconductor packages will still need to be installed accordingly.

Usage

See:

1. the Wiki (https://github.com/frihaka/deltaRpkm/wiki/Quick-Start-to-deltaRpkm) tab on the GitHub repo for a quick start
   
2. the test R script (doc/deltaRpkm_usage_example.R) to play with the main methods and parameters of the pipeline
   
3. the User Manual (doc/deltaRpkm_User_Manual.pdf) for a detailed tutorial
   

Note: if using more than 150 genomes, try rather with a machine with more RAM (>=16GB).