CeNet Omnibus An R/Shiny application to the construction and analysis of competing endogenous RNA network
Manual
How to Start
To install CeNetOmnibus package, please input the following commands in the console
devtools::install_github('GaoLabXDU/CeNetOmnibus')
CeNetOmnibus depends on multiple packages, including biomaRt, circlize, colourpicker, ComplexHeatmap, DT, formattable, ggplot2, ggplotify, ggthemr, gprofiler2, igraph, infotheo, jsonlite, linkcomm, MCL, parallel, PerformanceAnalytics, plyr, ProNet, R.oo, rhandsontable, scales, shiny, shinydashboard, shinyWidgets, survival, survminer, svglite, tibble, visNetwork.
To make sure all the dependency packages are installed, run following codes to install dependency packages.
library(CeNetOmnibus)
checkDependency()
Data Preparation
CeNet Omnibus demands users to upload four files for the constrction of ceRNA network, including
- The expression profiles of candidate ceRNAs and microRNAs
- The interaction between microRNA and candidate ceRNAs
- Essential information of candidate ceRNAs, eg. symbols, biotypes, and etc.
Get Start
The following commands should be used to start CeNet Omnibus.
library(CeNetOmnibus)
CeNetOmnibus()