A graphical user interface to facilitate the application of meta analysis on -Omics study
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")
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)
- 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 bebrew 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 forRSTUDIO_PANDOC
Sys.getenv("RSTUDIO_PANDOC")