caleb-huo / metaomics

Shiny GUI application for genomics meta-analysis

metaOmics

A graphical user interface to facilitate the application of meta analysis on -Omics study

Required package

preproc, metaClust, DT, shiny, shinyBS

• To install all the required packages, open R console

install.packages(c("utils", "devtools", "DMwR"))
source("https://bioconductor.org/biocLite.R")
biocLite("AnnotationDbi")

library(devtools)
install_github("metaOmic/MetaSparseKmeans")
install_github("metaOmic/preproc")

How to start the app

First, clone the project

git clone https://github.com/metaOmic/metaOmics

• in command line:

R -e "shiny::runApp('metaOmics', port=9987, launch.browser=T)"

• in R

shiny::runApp('metaOmics', port=9987, launch.browser=T)

How to start the documentation

• Install rmarkdown for R

instal.packages("rmarkdown")

• Inside doc directory, start R console, and:

rmarkdown::run(shiny_args=list(port=9988, launch.browser=T))

or in command line

R -e "rmarkdown::run(shiny_args=list(port=9988, launch.browser=T))"

• If you run into an issue with something like pandoc version 1.12.3 or higher is required and was not found., just install pandoc manually. For example, on Mac, it would be brew install pandoc. If you have Rstudio, you can also to get rstudio's pandoc environment. Go to rstudio console and find the system environment variable for RSTUDIO_PANDOC

Sys.getenv("RSTUDIO_PANDOC")