RBiomirGS - A simple to use package for miRNA gene set analysis, with miRNA-mRNA interaction searching and human mRNA orthologs conversion functionalities.
When using this program please cite: Zhang, J., & Storey, K. B. (2018). RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration. PeerJ, 6, e4262. PMID: 29340253.
Download and install R and R Studio. To install the latest version of RBiomirGS, please select the following commands (copy/paste) and run them in R Studio (make sure you are connected to the internet):
(1) Run the following command to install devtools (needed to run RBiomirGS), otherwise skip this step:
install.packages("devtools")(2) Run the following command to install Bioconductor (needed to run RBiomirGS), otherwise skip this step:
source("https://bioconductor.org/biocLite.R") biocLite() For help with installing Bioconductor, visit (https://www.bioconductor.org/install/)
(3) Run the following command to install RBiomirGS:
devtools::install_github("jzhangc/git_RBiomirGS/RBiomirGS", repos = BiocInstaller::biocinstallRepos())(4) To set a working directory use, replace
"..." with your folder address: For Windows:
setwd("working directory") For Mac and Linux:
setwd("working directory")The source code and the R package are available on GitHub: https://github.com/jzhangc/git_RBiomirGS
For a short RBiomirGS installation guide and user manual, download the following RBiomirGS Quick Start Guide .pdf
Sample input and output files
The files below are examples of input and output files from rbiomirGS using data from (Hadj-Moussa et al., 2016; PMID: 27090740):
DEMO- INPUT 1/2: RBiomirGS Sample Data (Monito liver miRNAs) .csv
DEMO- INPUT 2/2: RBiomirGS .gmt database files .zip (unzip the folder to retrieve the 3 .gmt database files)
DEMO- OUTPUT 1/3 - Histogram of all gene sets: RBiomirGS Histogram 1 .pdf
DEMO- OUTPUT 2/3 - Histogram of top 50 ranked KEGG pathways based on absolute value of the coefficient (with significant adjusted p values < 0.05): RBiomirGS Histogram 2 .pdf
DEMO- OUTPUT 3/3 - Volcano plot of all gene sets: RBiomirGS Volcano plot .pdf